CHD4 Sandbox: Difference between revisions
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<Structure load='6RYR' size='350' frame='true' align='right' caption='CHD4 (RCSB code [[6RYR]])' scene='88/880268/Chd4_model/2' /> | |||
<Structure load='6RYR' size='350' frame='true' align='right' caption='CHD4 (RCSB code [[6RYR]])' scene' / | |||
==Introduction== | ==Introduction== | ||
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==The Nucleosome== | ==The Nucleosome== | ||
The nucleosome is comprised of <scene name='88/880268/147-mer/2'>146-147 DNA base pairs</scene> wrapped around an <scene name='88/880268/147-mer_octamer/1'>octamer</scene> of four different proteins called histones. | The nucleosome is comprised of <scene name='88/880268/147-mer/2'>146-147 DNA base pairs</scene> wrapped around an <scene name='88/880268/147-mer_octamer/1'>octamer</scene> of four different proteins called histones. | ||
==The Histones== | |||
The four histone proteins: <scene name='88/880268/H4_in_complex/1'>H4</scene>, <scene name='88/880268/H3_histone/1'> H3</scene>, <scene name='88/880268/H2a_histone/1'> H2A</scene>, and <scene name='88/880268/H2b_histone/1'> H2B</scene> make up the nucleosome with two sets of two heterodimers<ref name=num2/>. Heterodimers consisting of H3 and H4 as well as H2A and H2B<ref name=num2>DOI 10.1080/21553769.2012.702667</ref>. These heterodimers form an octamer through the presence of hydrophobic interaction between dimers<ref name=num2/>. | The four histone proteins: <scene name='88/880268/H4_in_complex/1'>H4</scene>, <scene name='88/880268/H3_histone/1'> H3</scene>, <scene name='88/880268/H2a_histone/1'> H2A</scene>, and <scene name='88/880268/H2b_histone/1'> H2B</scene> make up the nucleosome with two sets of two heterodimers<ref name=num2/>. Heterodimers consisting of H3 and H4 as well as H2A and H2B<ref name=num2>DOI 10.1080/21553769.2012.702667</ref>. These heterodimers form an octamer through the presence of hydrophobic interaction between dimers<ref name=num2/>. | ||
==The Dyad Axis== | ==The Dyad Axis== | ||
The formation of the histones via hydrophobic interactions forms the octamer<ref name=num2/>. This octamer has dyad symmetry between the H3 and H3 histones, forming the dyad axis and referred to as super helical location 0 (SHL 0) <ref name=num2/>. | The formation of the histones via hydrophobic interactions forms the octamer<ref name=num2/>. This octamer has dyad symmetry between the H3 and H3 histones, forming the dyad axis and referred to as super helical location 0 (SHL 0) <ref name=num2/>. | ||
==Super Helical Position== | |||
The state of the minor groove directionality is referred to as SHL (Super Helical Location) <ref name=num2/>. With the DNA wrapping 1.65 turns around the nucleosome, the status of the minor groove conformation with respect to the orientation of the nucleosome with SHL 0 (the Dyad axis) <ref name=num2/>. It is to be noted that SHL positions can be both + and – but the position remains similar, as they reflect over the dyad axis at SHL 0<ref name=num2/>. The sign of the SHL is referring to which pole of the nucleosome the protein domain binds to on the DNA<ref name=num2/>. The directionality of the DNA bound to the nucleosome changes with the ± sign of the SHL as there is an enter and exit direction of the DNA on the nucleosome<ref name=num2/>. | The state of the minor groove directionality is referred to as SHL (Super Helical Location) <ref name=num2/>. With the DNA wrapping 1.65 turns around the nucleosome, the status of the minor groove conformation with respect to the orientation of the nucleosome with SHL 0 (the Dyad axis) <ref name=num2/>. It is to be noted that SHL positions can be both + and – but the position remains similar, as they reflect over the dyad axis at SHL 0<ref name=num2/>. The sign of the SHL is referring to which pole of the nucleosome the protein domain binds to on the DNA<ref name=num2/>. The directionality of the DNA bound to the nucleosome changes with the ± sign of the SHL as there is an enter and exit direction of the DNA on the nucleosome<ref name=num2/>. | ||
==Scaffolding of Histones for DNA== | ==Scaffolding of Histones for DNA== | ||
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The nucleosome is able to bind twice to CHD4 due to its symmetric duality with each SHL location roughly mirrored over the dyad axis<ref name=num1/>. A second CHD4 interaction with the nucleosome doesn’t change the complex’s stability or the DNA stability at SHL ± 7, the region of entrance and exit<ref name=num1/>. | The nucleosome is able to bind twice to CHD4 due to its symmetric duality with each SHL location roughly mirrored over the dyad axis<ref name=num1/>. A second CHD4 interaction with the nucleosome doesn’t change the complex’s stability or the DNA stability at SHL ± 7, the region of entrance and exit<ref name=num1/>. | ||
==Structure Information== | ==Structure Information== | ||
A 3.1 Å resolution model from cryo-EM. | A 3.1 Å resolution model from cryo-EM.<ref name=num1/> | ||
== References == | == References == | ||
<references/> | <references/> | ||
