Proteopedia - User contributions [en]

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T18:39:20Z

Aislin Vega Faust:

<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Drosophila nucleosome'>
== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA polymerase II moves down the strand of DNA, physically disrupting the contact between an H2A-H2B dimer and the core of the nucleosome, leading to H2A-H2B dimer eviction. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.

The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octameric Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight proteins, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During transcription, nucleosomes have been found to disassemble into hexasomes to allow RNA polymerase II to interact with the DNA, typically during elongation, stalling, or chromatin remodeling. Hexasomes contain a tetramer of H3-H4 dimers and one H2A-H2B dimer, with one H2B-H2A dimer present on octameric nucleosomes being absent. During stalling specifically, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.

Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II translocates and mechanical stress on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). Histones are a family of protiens that make up nucleosome cores and have similar characteristics. The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native Drosophila hexasome, one dimer of H2A/H2B is missing from the typical nucleosome octet, a function that aids other transcription factors in binding to the DNA.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexasome 9MU5</scene> is an NMR structure of a native Drosophila melanogaster nucleoprotein complex consisting of six histone proteins with a strand of DNA attached, composed of three dimer pairs. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA polymerase II during transcription. The two nucleic chains make up the ~147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and has fewer sites of contact to DNA than a nucleosome, making DNA more accessible.

== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019) that prevent aggregation. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene> around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold and follows characteristic structural motifs that define their family, consisting of three helices divided by two loops that allow them to fit together and dimerize.

The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are mostly <scene name='11/1109328/Charge/1'>positively charged</scene>, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidine. There are fewer residues bound to DNA in hexasomes than in <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022), potentially due to its ability to recognize asymmetric DNA exposure. INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes have been proposed to be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. An <scene name='11/1109328/9mu4_8cze/2'>overlay</scene> of octameric Drosophila and Xenopus nucleosome protein structures shows a general similarity with differences on the surface of the proteins where binding occurs wth DNA. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). There is currently no published literature associated with the Drosophila hexasome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene> to be included, but research about other nucleosomes from Drosophila and other animals is widely accessible, making this hexasome a useful tool for studying transcription machinery.

== References ==
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015

</StructureSection>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexosome

2026-05-07T18:22:04Z

Aislin Vega Faust: Aislin Vega Faust moved page T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexosome to T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome: Misspelled title

#REDIRECT [[T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome]]

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T18:22:04Z

<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Drosophila nucleosome'>
==A Native Drosophila melanogaster Hexasome With DNA Attached==

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA polymerase II moves down the strand of DNA, physically impeding the contact between an H2A-H2B dimer and nucleosome. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.

The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octameric Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During transcription, nucleosomes have been found to disassemble into hexasomes to allow RNA polymerase II to interact with the DNA, typically during elongation, stalling, or chromatin remodeling. Hexasomess contain a tetramer of H3-H4 dimers and one H2A-H2B dimer, with one H2B-H2A dimer present on octameric nucleosomes being absent. During stalling specifically, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native Drosophila hexasome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexasome 9MU5</scene> is an NMR structure of a native Drosophila melanogaster nucleoprotein complex consisting of six histone proteins with a strand of DNA attached. These are organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and has fewer sites of contact to DNA than a nucleosome, making DNA accessible.

== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. The dimerization and removal of histones from each other is aided by histone chaperoning proteins(Pardal, 2019). Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene> around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The individual proteins follow a characteristic structural motif that characterizes histones, consisting of three helices divided by two loops that allow them to fit together and dimerize.

The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are mostly <scene name='11/1109328/Charge/1'>positively charged</scene>, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidine. There are fewer residues bound to DNA on hexasomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022), likely due to its ability to recognize asymmetric DNA exposure. INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes have been proposed to be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. An <scene name='11/1109328/9mu4_8cze/2'>overlay</scene> of octameric Drosophila and Xenopus nucleosome protein structures shows a general similarity with differences on the surface of the proteins where binding occurs wth DNA. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). There is currently no published literature associated with the Drosophila hexasome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene> to be included.

== References ==
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015

</StructureSection>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T18:21:41Z

Aislin Vega Faust:

T:Aislin Vega Faust/Sandbox 1

2026-05-07T18:17:31Z

Aislin Vega Faust: Aislin Vega Faust moved page T:Aislin Vega Faust/Sandbox 1 to T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexosome

#REDIRECT [[T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexosome]]

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T18:17:31Z

Aislin Vega Faust: Aislin Vega Faust moved page T:Aislin Vega Faust/Sandbox 1 to T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexosome

<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Drosophila nucleosome'>
==A Native Drosophila melanogaster Hexameric Nucleosome With DNA Attached==

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA polymerase II moves down the strand of DNA, physically impeding the contact between an H2A-H2B dimer and nucleosome. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.

The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octameric Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During transcription, nucleosomes have been found to disassemble into hexasomes to allow RNA polymerase II to interact with the DNA, typically during elongation, stalling, or chromatin remodeling. Hexosomes are hexameric nucleosomes containing a tetramer of H3-H4 dimers and one H2A-H2B dimer, with one H2B-H2A dimer present on octameric nucleosomes being absent. During stalling specifically, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is an NMR structure of a native Drosophila melanogaster nucleoprotein complex consisting of six histone proteins with a strand of strand of DNA attatched. These are organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and has fewer sites of contact to DNA than a nucleosome, making DNA accessible.

== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. The dimerization to and removal of histones from each other is aided by histone chaperoning proteins(Pardal, 2019). Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene> around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The individual proteins follow a characteristic structural motif that characterize histones, consisting of three helices divided by two loops that allow them to fit together and dimerize.

The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are mostly <scene name='11/1109328/Charge/1'>positively charged</scene>, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidine. There are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022), likely due to its ability to recognize asymmetric DNA exposure. INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes have been proposed to be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. An <scene name='11/1109328/9mu4_8cze/2'>overlay</scene> of octameric Drosophila and Xenopus nucleosome protein structures shows a general similarity with differences on the surfaceof the proteins where binding occurs wth DNA. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene> has no published literature.

== References ==
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015

</StructureSection>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T18:13:36Z

Aislin Vega Faust:

<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Drosophila nucleosome'>
==A Native Drosophila melanogaster Hexameric Nucleosome With DNA Attached==

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA polymerase II moves down the strand of DNA, physically impeding the contact between an H2A-H2B dimer and nucleosome. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.

The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octameric Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During transcription, nucleosomes have been found to disassemble into hexasomes to allow RNA polymerase II to interact with the DNA, typically during elongation, stalling, or chromatin remodeling. Hexosomes are hexameric nucleosomes containing a tetramer of H3-H4 dimers and one H2A-H2B dimer, with one H2B-H2A dimer present on octameric nucleosomes being absent. During stalling specifically, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is an NMR structure of a native Drosophila melanogaster nucleoprotein complex consisting of six histone proteins with a strand of strand of DNA attatched. These are organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and has fewer sites of contact to DNA than a nucleosome, making DNA accessible.

== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. The dimerization to and removal of histones from each other is aided by histone chaperoning proteins(Pardal, 2019). Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene> around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The individual proteins follow a characteristic structural motif that characterize histones, consisting of three helices divided by two loops that allow them to fit together and dimerize.

The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are mostly <scene name='11/1109328/Charge/1'>positively charged</scene>, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidine. There are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022), likely due to its ability to recognize asymmetric DNA exposure. INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes have been proposed to be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. An <scene name='11/1109328/9mu4_8cze/2'>overlay</scene> of octameric Drosophila and Xenopus nucleosome protein structures shows a general similarity with differences on the surfaceof the proteins where binding occurs wth DNA. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene> has no published literature.

== References ==
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015

</StructureSection>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T17:55:25Z

Aislin Vega Faust:

<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Drosophila nucleosome'>
==A Native Drosophila melanogaster Hexameric Nucleosome With DNA Attached==

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octameric Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During transcription, nucleosomes have been found to disassemble into hexasomes to allow RNA Polymerase II to interact with the DNA, typically during elongation, stalling, or chromatin remodeling. During stalling specifically, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and has fewer sites of contact to DNA than a nucleosome.

== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene> around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are mostly <scene name='11/1109328/Charge/1'>positively charged</scene>, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidine. There are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes have been proposed to be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. An <scene name='11/1109328/9mu4_8cze/2'>overlay</scene> of octameric Drosophila and Xenopus nucleosome protein structures shows a general similarity with differences on the surfaceof the proteins where binding occurs wth DNA. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene> has no published literature.

== References ==
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015

</StructureSection>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T16:58:18Z

Aislin Vega Faust:

<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Drosophila nucleosome'>
==A Native Drosophila melanogaster Hexameric Nucleosome With DNA Attached==

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.

== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. An <scene name='11/1109328/9mu4_8cze/2'>overlay</scene> of octomeric Drosophila and Xenopus nucleosome protein structures shows a general similarity with differences on the outside of the proteins where binding occurs. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015

</StructureSection>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T16:57:18Z

Aislin Vega Faust:

<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Drosophila nucleosome'>
==A Native Drosophila melanogaster Hexameric Nucleosome With DNA Attached==

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. An <scene name='11/1109328/9mu4_8cze/2'>overlay</scene> of octomeric Drosophila and Xenopus nucleosome protein structures shows a general similarity with differences on the outside of the proteins where binding occurs. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>
</StructureSection>

File:8CZE match 9MU5.pdb

2026-05-07T15:47:24Z

Aislin Vega Faust: PDB of 8CZE matchmade to 9MU5 in ChimeraX.

== Summary ==
PDB of 8CZE matchmade to 9MU5 in ChimeraX.

File:8CZEand9MU5 loadable.txt

2026-05-07T15:34:43Z

Aislin Vega Faust: 8CZE and 9MU%, but smaller.

== Summary ==
8CZE and 9MU%, but smaller.

File:8CZEand9MU5.txt

2026-05-07T15:07:48Z

Aislin Vega Faust: 8CZE and 9MU5 combined from RSCB.

== Summary ==
8CZE and 9MU5 combined from RSCB.

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T14:43:27Z

Aislin Vega Faust:

<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Drosophila nucleosome'>
==A Native Drosophila melanogaster Hexameric Nucleosome With DNA Attached==

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>
</StructureSection>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T14:42:18Z

Aislin Vega Faust:

<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Drosophila nucleosome'>

</StructureSection>
==A Native Drosophila melanogaster Hexameric Nucleosome With DNA Attached==

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>
</StructureSection>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T14:37:09Z

Aislin Vega Faust:

<applet load='9Mu5' scene='11/1109328/Newdefault/1' size='340' align='right' caption='Native Drosophila nucleosome' />
==A Native Drosophila melanogaster Hexameric Nucleosome With DNA Attached==
== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T14:17:35Z

Aislin Vega Faust:

<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Drosophila nucleosome'></StructureSection>
==A Native Drosophila melanogaster Hexameric Nucleosome With DNA Attached==
== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T14:16:30Z

Aislin Vega Faust:

{{StructureSection

|load=9Mu5
|scene=11/1109328/Newdefault/1
|size=340

|side=right
|caption=Native Drosophila nucleosome
}}
==A Native Drosophila melanogaster Hexameric Nucleosome With DNA Attached==
== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T14:13:00Z

Aislin Vega Faust:

<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Hexameric Drosophila nucleosome'></StructureSection>
==A Native Drosophila melanogaster Hexameric Nucleosome With DNA Attached==
== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T14:10:33Z

Aislin Vega Faust:

==A native Drosophila melanogaster hexameric nucleosome with DNA attached==
<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Hexameric Drosophila nucleosome'></StructureSection>

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T14:08:38Z

Aislin Vega Faust:

==A native Drosophila melanogaster hexameric nucleosome with DNA attached==
<StructureSection load='9Mu5' scene='11/1109328/Newdefault/1' size='340' side='right' caption='Native Hexameric Drosophila Nucleosome'> </StructureSection>

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T14:08:09Z

Aislin Vega Faust:

==A native Drosophila melanogaster hexameric nucleosome with DNA attached==
<StructureSection load='9Mu5' scene='Newdefault/1' size='340' side='right' caption='Native Hexameric Drosophila Nucleosome'> </StructureSection>

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T14:07:17Z

Aislin Vega Faust:

==A native Drosophila melanogaster hexameric nucleosome with DNA attached==
<StructureSection load='9Mu5' scene='NewDefault' size='340' side='right' caption='Native Hexameric Drosophila Nucleosome'> </StructureSection>

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T13:48:26Z

Aislin Vega Faust:

==A native Drosophila melanogaster hexameric nucleosome with DNA attached==
<StructureSection load='9Mu5' size='340' side='right' caption='Native Drosophila nucleosome' ''>
</StructureSection>

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription as RNA Polymerase II moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNA Polymerase II stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, the chromatin structure must be regulated, as the compact shape prevents RNA polymerase II from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNA Polymerase II to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNA Polymerase II to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNA Polymerase II torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3, each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNA Polymerase II during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are <scene name='11/1109328/Charge/1'>positively charged</scene> overall, allowing negatively charged DNA to be attracted and bind. This charge is the result of histones being rich in <scene name='11/1109328/Hexasome_charge/1'>positively charged amino acids</scene> like lysine, arginine, and histidineThere are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to mobilize rapidly and position hexasomes, allowing transcription to proceed more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools for deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for the natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-07T13:36:17Z

Aislin Vega Faust:

==A native Drosophila melanogaster hexameric nucleosome with DNA attached==
<StructureSection load='9Mu5' size='340' side='right' caption='Native Drosophila nucleosome' ''>
</StructureSection>

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription, as RNA Polymerase II, or RNAPII moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNAPII stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, it is important that the chromatin structure is regulated, as the compact shape prevents PRNAII from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNAPII to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNAPII to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNAPII torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3 each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNAPII during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/2'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are overall <scene name='11/1109328/Hexasome_charge/1'>positively charged</scene>, allowing negatively charged DNA to be attracted and bind. There are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to rapidly mobilize and position hexasomes, allowing for transcription to be done more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools to deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-01T03:47:35Z

Aislin Vega Faust:

==A native Drosophila melanogaster hexameric nucleosome with DNA attached==
<StructureSection load='9Mu5' size='340' side='right' caption='Native Drosophila nucleosome' ''>
</StructureSection>

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription, as RNA Polymerase II, or RNAPII moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNAPII stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, it is important that the chromatin structure is regulated, as the compact shape prevents PRNAII from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNAPII to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNAPII to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNAPII torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3 each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNAPII during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/1'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are overall <scene name='11/1109328/Hexasome_charge/1'>positively charged</scene>, allowing negatively charged DNA to be attracted and bind. There are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to rapidly mobilize and position hexasomes, allowing for transcription to be done more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools to deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-01T03:41:51Z

Aislin Vega Faust:

==A native Drosophila melanogaster hexameric nucleosome with DNA attached==
<StructureSection load='9Mu5' size='340' side='right' caption='Native Drosophila nucleosome' ''>
</StructureSection>

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription, as RNA Polymerase II, or RNAPII moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNAPII stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, it is important that the chromatin structure is regulated, as the compact shape prevents PRNAII from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNAPII to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNAPII to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNAPII torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3 each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNAPII during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/1'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are overall <scene name='11/1109328/Hexasome_charge/1'>positively charged</scene>, allowing negatively charged DNA to be attracted and bind. There are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to rapidly mobilize and position hexasomes, allowing for transcription to be done more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools to deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

<scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene>
<scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene>

<scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene>
<scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>
<scene name='11/1109328/Drosophila_h3_h4_dimer_b/1'>H3B-H4B</scene>

<scene name='11/1109328/H2a_h2b_binding/1'>H2A-H2B binding surfaces</scene>

<scene name='11/1109328/Hexasome_binding/1'>bound to 9MU5</scene>
<scene name='11/1109328/Nucleosome_binding/2'>bount to 9MU4</scene>
<scene name='11/1109328/Hexasome_charge/1'>hexasome is positively charged</scene>

<scene name='11/1109328/Human_ino80/1'>INO80</scene>

<scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-01T03:37:52Z

Aislin Vega Faust:

==A native Drosophila melanogaster hexameric nucleosome with DNA attached==
<StructureSection load='9Mu5' size='340' side='right' caption='Native Drosophila nucleosome' ''>
Structure 9MU5 '''T:Aislin Vega Faust/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription, as RNA Polymerase II, or RNAPII moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNAPII stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, it is important that the chromatin structure is regulated, as the compact shape prevents PRNAII from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNAPII to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNAPII to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNAPII torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3 each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Overall Structure ==
This <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene> is made up of six histone protein chains organized into three dimers, as well as two nucleic acid chains. Two of these dimers, each <scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>, are made up of histones H3 and H4, while the other dimer is made of histones H2A and H2B. The <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> histone present is located distal to RNAPII during transcription. The two nucleic chains make up the 147 bp-long DNA strand attached to the nucleosome. Because one dimer is missing from the typical octameric form, the DNA is wrapped asymmetrically and loosely in comparison to that of a nucleosome.
== Binding Sites and Interactions ==
Because this is a nucleoprotein complex and not a single protein, there are many binding sites within the structure. Each histone is dimerized with another. Histone H3 is dimerized with histone H4, and the dimer is bound to a second copy of itself to form a tetramer. Histone H2A is dimerized with histone H2B, and this dimer joins the H3-H4 tetramer to form a hexamer. For example, a portion of histone H2B is <scene name='11/1109328/H2a_h2b_binding/1'>wrapped</scene>around H2A. The binding sites of each histone, for the purpose of assembling a hexasome, are large faces that take up the majority of the proteins. Each histone has a histone fold, a secondary structural motif that characterizes most histone proteins. The proteins follow a helix-turn-helix-turn-helix structure that allows them to fit together and dimerize. The dimerization of histones to each other is aided by histone chaperoning proteins(Pardal, 2019).
The <scene name='11/1109328/Hexasome_binding/1'>binding sites of the hexasome to DNA</scene> are spread across the perimeter of the nucleoprotein complex, allowing for the strand to wrap around the entire structure. The hexasomes and the nucleosomes that become them are overall <scene name='11/1109328/Hexasome_charge/1'>positively charged</scene>, allowing negatively charged DNA to be attracted and bind. There are fewer residues bound to DNA on hexosomes than <scene name='11/1109328/Nucleosome_binding/2'>octametric nucleosomes</scene>, both because hexasomes are smaller and to allow the activity of other transcription factors. Depending on the hexasome or nucleosome, there may be additional ligands or interactions.

== Current Research ==
Some hexasomes are the preferred substrate of <scene name='11/1109328/Human_ino80/1'>INO80</scene>, an ATP-dependent chromatin remodeling complex. Chromatin remodeling complexes slide and alter hexasomes and nucleosomes to aid in transcription, changing their placement and tension on the DNA strand. INO80 has been found to rapidly mobilize and position hexasomes, allowing for transcription to be done more quickly (Hsieh, 2022). INO80 has been found to slide hexasomes as efficiently as it does nucleosomes (Aggarwal, 2026). Hexasomes and other transcription intermediates are important tools to deciphering how and why chromatin is remodeled. Some ATP-dependent protein remodeling complexes may even be capable of catalyzing the exchange of <scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene> dimers between nucleosomes(Bruno, 2003), allowing cells to manipulate chromatin structure manually.

== Additional Findings ==
Drosophila nucleosomes have been used to study nucleosome divergence. Nucleosomes are polymorphic and diverse across species, but are also highly conserved even between vertebrates and invertebrates. In particular, they are compared to the nucleosomes of <scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>. Their sequences have been used to provide evidence for natural selection of nucleosome genes. Drosophila have unique nucleosome systems, and they do not incorporate H2A.Z into certain nucleosomes(Langley, 2014). The literature associated with the Drosophila hexameric nucleosome <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>9MU5</scene>are unpublished.

<scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene>
<scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene>

<scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene>
<scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>
<scene name='11/1109328/Drosophila_h3_h4_dimer_b/1'>H3B-H4B</scene>

<scene name='11/1109328/H2a_h2b_binding/1'>H2A-H2B binding surfaces</scene>

<scene name='11/1109328/Hexasome_binding/1'>bound to 9MU5</scene>
<scene name='11/1109328/Nucleosome_binding/2'>bount to 9MU4</scene>
<scene name='11/1109328/Hexasome_charge/1'>hexasome is positively charged</scene>

<scene name='11/1109328/Human_ino80/1'>INO80</scene>

<scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>

== References ==
<
Aggarwal, P., Sharma, M., Woike, S., Kunert, F., Brem, A., Moldt, M., & Hopfner, K. (2026). Recognition and remodelling of nucleosomes and hexasomes by the human INO80 complex. Nucleic Acids Research, 54(5). https://doi.org/10.1093/nar/gkag138

Brahmachari, S., Tripathi, S., Onuchic, J. N., & Levine, H. (2024). Nucleosomes play a dual role in regulating transcription dynamics. Proceedings of the National Academy of Sciences, 121(28), e2319772121. https://doi.org/10.1073/pnas.2319772121

Brown, D. T. (2001). Histone variants: are they functionally heterogeneous? Genome Biology, 2(7), reviews0006.1. https://doi.org/10.1186/gb-2001-2-7-reviews0006

Bruno, M., Flaus, A., Stockdale, C., Rencurel, C., Ferreira, H., & Owen-Hughes, T. (2003). Histone H2A/H2B dimer exchange by ATP-Dependent Chromatin Remodeling Activities. Molecular Cell, 12(6), 1599–1606. https://doi.org/10.1016/s1097-2765(03)00499-4

Clapier, C. R., Chakravarthy, S., Petosa, C., Fernández‐Tornero, C., Luger, K., & Müller, C. W. (2007). Structure of the Drosophila nucleosome core particle highlights evolutionary constraints on the H2A‐H2B histone dimer. Proteins Structure Function and Bioinformatics, 71(1), 1–7. https://doi.org/10.1002/prot.21720

Hsieh, L. J., Gourdet, M. A., Moore, C. M., Muñoz, E. N., Gamarra, N., Ramani, V., & Narlikar, G. J. (2022). A hexasome is the preferred substrate for the INO80 chromatin remodeling complex, allowing versatility of function. Molecular Cell, 82(11), 2098-2112.e4. https://doi.org/10.1016/j.molcel.2022.04.026

Langley, S. A., Karpen, G. H., & Langley, C. H. (2014). Nucleosomes shape DNA polymorphism and divergence. PLoS Genetics, 10(7), e1004457. https://doi.org/10.1371/journal.pgen.1004457

Mavrich, T. N., Jiang, C., Ioshikhes, I. P., Li, X., Venters, B. J., Zanton, S. J., Tomsho, L. P., Qi, J., Glaser, R. L., Schuster, S. C., Gilmour, D. S., Albert, I., & Pugh, B. F. (2008). Nucleosome organization in the Drosophila genome. Nature, 453(7193), 358–362. https://doi.org/10.1038/nature06929

Pardal, A. J., Fernandes-Duarte, F., & Bowman, A. J. (2019). The histone chaperoning pathway: from ribosome to nucleosome. Essays in Biochemistry, 63(1), 29–43. https://doi.org/10.1042/ebc20180055

Ramachandran, S., Ahmad, K., & Henikoff, S. (2017). Transcription and remodeling produce asymmetrically unwrapped nucleosomal intermediates. Molecular Cell, 68(6), 1038-1053.e4. https://doi.org/10.1016/j.molcel.2017.11.015
>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-01T03:26:47Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-01T03:07:11Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-01T03:06:29Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-01T03:05:49Z

Aislin Vega Faust:

==Sandbox 1==
<StructureSection load='9Mu5' size='340' side='right' caption='Native Drosophila nucleosome' ''>
This is a default text for your page '''T:Aislin Vega Faust/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Introduction==
This is the solved structure of the native Drosophila melanogaster <scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Hexameric Nucleosome 9MU5</scene>, or hexasome, with a strand of DNA attached. Nucleosomes are located in the nucleus of cells and are the structural basis for chromatin. Hexasomes, or hexameric nucleosomes, are non-canonical structures present in the nucleus of cells, primarily involved in regulating transcription. Nucleosomes become hexasomes naturally through transcription, as RNA Polymerase II, or RNAPII moves down the strand of DNA. This hexasome is missing the proximal H2A-H2B dimer that makes typical nucleosomes octets, meaning it is likely the result of RNAPII stalling during the transcription process. Hexasomes aid in transcription by making room for other factors like PRNAII, and they are also preferred substrates for some transcription factors like INO80.
The core of an <scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene> is an octamer consisting of eight histones, which DNA wraps around to form chromatin, the efficient and organized structure that makes up chromosomes. During transcription, it is important that the chromatin structure is regulated, as the compact shape prevents PRNAII from binding and functioning. During different transcription steps, nucleosomes have been found to disassemble differently into hexasomes to allow RNAPII to interact with the DNA. During stalling, the proximal H2A-H2B dimer is lost, and during elongation, the distal H2A-H2B dimer is lost. Hexasomes are smaller than octet nucleosomes, making room for RNAPII to complete transcription, and are even the preferred substrate of certain transcription factors like the INO80 remodeling complex.
Octameric nucleosomes become hexasomes naturally through transcription. As RNAPII torque on the strand of DNA increases, the H2A/H2B dimers are often lost. The eight histones that provide the core structure for nucleosomes are functionally heterogeneous (Brown, 2001). The nucleosome histone octet is composed of four histone dimers. There are two copies of histone H2A, which are each dimers to a copy of histone H2B, and two copies of histone H3 each dimerized with H4. In the native hexameric Drosophila nucleosome, one dimer of H2A/H2B is missing from the typical nucleosome octet.

== Disease ==

== Relevance ==

== Structural highlights ==

<scene name='11/1109328/H2a_h2b_dimer/3'>H2A-H2B</scene>

<scene name='11/1109328/Drosophila_nucleosome_9mu5/1'>Drosophila Hexameric Nucleosome 9MU5</scene>

<scene name='11/1109328/Drosophila_nucleosome_9mu4/1'>Octometic Drosophila Nucleosome 9MU4</scene>

<scene name='11/1109328/Drosophila_h3_h4_dimer_a/1'>H3A-H4B</scene>

<scene name='11/1109328/Drosophila_h3_h4_dimer_b/1'>H3B-H4B</scene>
This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene>

<scene name='11/1109328/Hexasome_binding/1'>bound to 9MU5</scene>

<scene name='11/1109328/Nucleosome_binding/2'>bount to 9MU4</scene>

<scene name='11/1109328/H2a_h2b_binding/1'>H2A-H2B binding surfaces</scene>

by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>

<scene name='11/1109328/Hexasome_charge/1'>hexasome is positively charged</scene>

<scene name='11/1109328/Human_ino80/1'>INO80</scene>

<scene name='11/1109328/Xenopus_laevis/2'>Xenopus laevis</scene>

== References ==
<references/>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-01T03:01:47Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-01T02:56:04Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-05-01T02:52:18Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T23:56:28Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T23:49:04Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T15:50:11Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T15:34:19Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T15:17:59Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T14:41:24Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T14:39:34Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T14:29:36Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T14:28:55Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T03:50:42Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T03:48:38Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T03:43:18Z

Aislin Vega Faust:

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-30T02:09:50Z

Aislin Vega Faust:

==Sandbox 1==
<StructureSection load='9Mu5' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''T:Aislin Vega Faust/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

<scene name='11/1109328/H2a_h2b_dimer/1'>H2A-H2B</scene>

This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene> by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-29T13:36:42Z

Aislin Vega Faust:

==Sandbox 1==
<StructureSection load='9Mu5' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''T:Aislin Vega Faust/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene> by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

T:Aislin Vega Faust/DNA Bound Native Drosophila melanogaster Hexasome

2026-04-29T12:56:34Z

Aislin Vega Faust: Created page with "==Sandbox 1== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for your page '''T:Aislin Vega Faust/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. == Fu..."

==Sandbox 1==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''T:Aislin Vega Faust/Sandbox 1'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name='10/1070530/1stp_coloerd/1'>color</scene> by Group, and another to make <scene name='10/1070530/1stp_transparency/1'>a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>