Proteopedia - User contributions [en]

User:Michele White/Sandbox 1

2013-11-18T00:30:18Z

Michele White:

<StructureSection load='1dx5' size='350' side='center' caption='Thrombin-TM (PDB entry [[1dx5]])' scene=''>

== Test ==

<scene name='56/568921/Abe1/1'>ABE1</scene>
<scene name='56/568921/Abe1_and_active_site/1'>ABE1 and active site</scene>

User:Michele White/Sandbox 1

2013-11-18T00:18:37Z

Michele White:

User:Michele White/Sandbox 1

2013-11-16T21:16:57Z

Michele White:

<StructureSection load='1dx5' size='350' side='center' caption='Thrombin-TM (PDB entry [[1dx5]])' scene=''>

== Test ==

User:Michele White/Sandbox 1

2013-11-16T21:16:12Z

Michele White: New page: <StructureSection load='1dx5' size='350' side='center' caption='Thrombin-TM (PDB entry 1dx5)' scene=''>

User:Michele White

2013-11-16T21:14:15Z

Michele White:

* Full Real Name: Michele White

* Position: Full time student and student researcher of protein chemistry

* Institution (NO ABBREVIATIONS): University of Tennessee, Knoxville

* City, State/Province, Country: Knoxville, TN, USA

* Field of Expertise or Study: Senior at University of Tennessee studying biochemistry, cellular, and molecular biology. Researching functional dynamic of cytochrome p450 enzymes

*[[User:Michele White/Sandbox 1]]

NF-Y Transcription Factor Sandbox

2013-11-07T16:08:34Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of NF-Y Transcription Factor with DNA (PDB entry [[4awl]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences and can either repress or activate the transcription of a gene. TFs have a diverse family of proteins and normally exist in a multisubunit complex. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. In plants, the NF-Y transcription factors regulate and respond to many physiological responses. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene>({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}) that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_finallll_linker/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Protein Function ==

The post-translational modifications (PTMs) that NF-Y transcription factor is associated with aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

 The NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>ionic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). Interaction between NF-Y and DNA can be blocked by drugs that bind to the minor groove.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T14:58:19Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences and can either repress or activate the transcription of a gene. TFs have a diverse family of proteins and normally exist in a multisubunit complex. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. In plants, the NF-Y transcription factors regulate and respond to many physiological responses. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_finallll_linker/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

 The NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). Interaction between NF-Y and DNA can be blocked by drugs that bind to the minor groove.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T14:57:35Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences and can either repress or activate the transcription of a gene. TFs have a diverse family of proteins and normally exist in a multisubunit complex. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. In plants, the NF-Y transcription factors regulate and respond to many physiological responses. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker_new/1'>A1A2 linker</scene> <scene name='56/566534/A1a2_linker_final/1'>A1A2 linker</scene>
<scene name='56/566534/A1a2_finallll_linker/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

 The NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). Interaction between NF-Y and DNA can be blocked by drugs that bind to the minor groove.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T14:49:44Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences and can either repress or activate the transcription of a gene. TFs have a diverse family of proteins and normally exist in a multisubunit complex. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. In plants, the NF-Y transcription factors regulate and respond to many physiological responses. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker_new/1'>A1A2 linker</scene> <scene name='56/566534/A1a2_linker_final/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

 The NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). Interaction between NF-Y and DNA can be blocked by drugs that bind to the minor groove.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T14:45:04Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences and can either repress or activate the transcription of a gene. TFs have a diverse family of proteins and normally exist in a multisubunit complex. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. In plants, the NF-Y transcription factors regulate and respond to many physiological responses. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker_new/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

 The NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). Interaction between NF-Y and DNA can be blocked by drugs that bind to the minor groove.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T14:44:02Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences and can either repress or activate the transcription of a gene. TFs have a diverse family of proteins and normally exist in a multisubunit complex. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. In plants, the NF-Y transcription factors regulate and respond to many physiological responses. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene>
<scene name='56/566534/A1a2_linker_new/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

 The NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). Interaction between NF-Y and DNA can be blocked by drugs that bind to the minor groove.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T14:37:53Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences and can either repress or activate the transcription of a gene. TFs have a diverse family of proteins and normally exist in a multisubunit complex. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. In plants, the NF-Y transcription factors regulate and respond to many physiological responses. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

 The NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). Interaction between NF-Y and DNA can be blocked by drugs that bind to the minor groove.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T14:36:40Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences and can either repress or activate the transcription of a gene. TFs have a diverse family of proteins and normally exist in a multisubunit complex. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. In plants, the NF-Y transcription factors regulate and respond to many physiological responses. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). Interaction between NF-Y and DNA can be blocked by drugs that bind to the minor groove.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T14:07:43Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences and can either repress or activate the transcription of a gene. TFs have a diverse family of proteins and normally exist in a multisubunit complex. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref> in mammals. In plants, the NF-Y transcription factors regulate and respond to many physiological responses. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). Interaction between NF-Y and DNA can be blocked by drugs that bind to the minor groove.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T14:00:23Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref> in mammals. In plants, the NF-Y transcription factors regulate and respond to many physiological responses. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). Interaction between NF-Y and DNA can be blocked by drugs that bind to the minor groove.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T13:57:19Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref> in mammals. In plants, the NF-Y transcription factors regulate and respond to many physiological responses. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}).

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T06:28:31Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. <scene name='56/566534/Nf-y_ccaat_specific_residues/1'>Arg274 and His277</scene> residues interacting with the CCAAT box prevent G bases due to steric reasons, and these residues perform specific interactions that link the NF-Y/DNA complex. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}).

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T05:31:13Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}} {{Template:ColorKey_Polar}}).

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T05:30:24Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}{{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}).

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T05:29:56Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.

 The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}).

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T05:29:23Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer.
The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}).

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T05:28:23Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>
== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===

NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}).

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T05:25:40Z

Michele White:

<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==
The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}).

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T05:24:46Z

Michele White: /* Overview */

== Overview ==
<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==
The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}).

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T05:24:11Z

Michele White:

== Overview ==
<StructureSection load='4awl' size='350' side='right' caption='Structure of Variola Topoisomerase 1B with DNA (PDB entry [[3igc]])' scene=''>

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==
{{STRUCTURE_4awl| PDB=4awl | SCENE= }}
The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}).

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T05:21:51Z

Michele White: /* DNA Interaction */

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==
{{STRUCTURE_4awl| PDB=4awl | SCENE= }}
The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. Van der Waals and <scene name='56/566534/Nf-y_dna_complex/1'>electrostatic interactions</scene> provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}).

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T05:20:35Z

Michele White: /* DNA Interaction */

NF-Y Transcription Factor Sandbox

2013-11-07T05:03:40Z

Michele White: /* DNA Interaction */

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==
{{STRUCTURE_4awl| PDB=4awl | SCENE= }}
The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC histone folding domain (HFD) dimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />. Van der Waals and electrostatic interactions provide the stabilization of the NF-Y/DNA complex due to the highly basic surface of the NF-YB/NF-YC HFD dimer and negatively charged DNA<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T04:57:31Z

Michele White: /* Protein Structure */

NF-Y Transcription Factor Sandbox

2013-11-07T04:54:47Z

Michele White: /* Overview */

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins through translation. NF-Y is a transcription factor involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==
{{STRUCTURE_4awl| PDB=4awl | SCENE= }}
The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T04:50:02Z

Michele White: /* Protein Structure */

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is one type of the many types transcription factor. NF-Y is a protein involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==
{{STRUCTURE_4awl| PDB=4awl | SCENE= }}
The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene> that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T04:49:20Z

Michele White: /* Protein Structure */

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is one type of the many types transcription factor. NF-Y is a protein involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==
{{STRUCTURE_4awl| PDB=4awl | SCENE= }}
The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene>that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />({{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T04:48:32Z

Michele White: /* Protein Structure */

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is one type of the many types transcription factor. NF-Y is a protein involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==
{{STRUCTURE_4awl| PDB=4awl | SCENE= }}
The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene>that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the
<scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.
{{Template:ColorKey_Hydrophobic}}
{{Template:ColorKey_Polar}}

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T04:43:51Z

Michele White: /* Protein Structure */

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is one type of the many types transcription factor. NF-Y is a protein involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==
{{STRUCTURE_4awl| PDB=4awl | SCENE= }}
The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. <scene name='56/566534/Hydrophobic_residues/1'>Hydrophobic residues</scene>that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the
<scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T04:12:27Z

Michele White: /* Protein Structure */

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is one type of the many types transcription factor. NF-Y is a protein involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==
{{STRUCTURE_4awl| PDB=4awl | SCENE= }}
The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the
<scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T04:11:51Z

Michele White:

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is one type of the many types transcription factor. NF-Y is a protein involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==
{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the
<scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T04:11:19Z

Michele White: /* Protein Structure */

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is one type of the many types transcription factor. NF-Y is a protein involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya_real/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb_real/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc_real/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. The composition of mostly α-helices gives the protein flexibility. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the
<scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T04:04:14Z

Michele White: /* Protein Structure */

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is one type of the many types transcription factor. NF-Y is a protein involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the
<scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T04:02:09Z

Michele White: /* Overview */

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is one type of the many types transcription factor. NF-Y is a protein involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

Certain subunits of NF-Y (NF-YB and NF-YC) contain amino acids similar to those found in HFDs <ref name="activation" />. The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the
<scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.
 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T04:00:59Z

Michele White: /* NF-Y Transcription Factor */

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Overview ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is one type of transcription factor. NF-Y is a protein involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

Certain subunits of NF-Y (NF-YB and NF-YC) contain amino acids similar to those found in HFDs <ref name="activation" />. The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the
<scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.
 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T03:36:18Z

Michele White:

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== NF-Y Transcription Factor ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is one type of transcription factor. NF-Y is a protein involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />.

== Protein Structure ==

Certain subunits of NF-Y (NF-YB and NF-YC) contain amino acids similar to those found in HFDs <ref name="activation" />. The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the
<scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.
 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.

===DNA Interaction===
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-07T03:29:38Z

Michele White:

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Protein Structure ==

NF-Y subunits are closely related to core histones. A histone is a conserved protein that wraps 146 nucleotides of DNA into the basic unit of chromatin, the nucleosome <ref name="activation" />. Histone-fold Domains (HFDs) are required for the tertiary structure of histones and non-sequence specific contacts with DNA<ref name="activation" />. Certain subunits of NF-Y (NF-YB and NF-YC) contain amino acids similar to those found in HFDs <ref name="activation" />. The NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the
<scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.
 Furthermore, the NF-Y gene can be deferentially spliced to provide different isoforms of the protein. <ref name="activation" />. For example, NF-YA has two isoforms, which differ in the amount of amino acids in the glutamine (Q)-rich activation domain<ref name="activation">PMID: 22050321</ref>. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time<ref name="activation" />. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability<ref name="activation" />.

== Protein Function ==

A [https://en.wikipedia.org/wiki/Transcription_factor transcription factor] (TF) is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is one type of transcription factor. NF-Y is a protein involved in histone [https://en.wikipedia.org/wiki/Posttranslational_modification post-translational modifications] (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. These PTMs aid in identifying regions of DNA that are destined to be transcribed. NF-Y is responsible for recruiting enzymes responsible for transcription (like RNA Polymerase II), and enzymes involved in acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications <ref name="activation" />. Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters<ref name="mainarticle" />.
NF-Y is regulated by redox mechanisms<ref name="oxidativeredox">PMID: 19965775</ref>. The regulated subunit (NF-YB) has three conserved cysteines in its A2 helix: <scene name='56/566534/Cys_83/3'>C83</scene>, <scene name='56/566534/Cys_87/1'>C87</scene>, and <scene name='56/566534/Cys103/1'>C103</scene>; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation<ref name="oxidativeredox" />.
NF-Y interacts with DNA in several ways; one particular way is by using the C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box<ref name="mainarticle" />.

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-06T18:24:01Z

Michele White: /* Protein Structure */

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Protein Function ==

NF-Y is a transcription factor (TF), which is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is an important protein involved in histone posttranslational modifications (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. These PTMs aid in regions of the DNA that are destined to be transcribed. NF-Y is also involved in recruiting enzymes responsible for acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications (reference here). Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters.
 NF-Y has two isoforms, which differ in the amount of amino acids in the Q-rich activation domain. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability (reference hereee).
 NF-Y is regulated by redox mechanisms. The regulated subunit has three conserved Cysteines in the A2 helix: C83, C87, and C103; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation(referenceeeee).

== Protein Structure ==

NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the
<scene name='56/566534/A1a2_linker/2'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Interaction With DNA ==

The C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box. An important residue in the catalytic site is <scene name='56/566534/Lysine_138/1'>Lys138</scene>

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-06T18:13:31Z

Michele White: /* Protein Structure */

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Protein Function ==

NF-Y is a transcription factor (TF), which is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is an important protein involved in histone posttranslational modifications (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. These PTMs aid in regions of the DNA that are destined to be transcribed. NF-Y is also involved in recruiting enzymes responsible for acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications (reference here). Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters.
 NF-Y has two isoforms, which differ in the amount of amino acids in the Q-rich activation domain. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability (reference hereee).
 NF-Y is regulated by redox mechanisms. The regulated subunit has three conserved Cysteines in the A2 helix: C83, C87, and C103; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation(referenceeeee).

== Protein Structure ==

NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle" />. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle" />. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Interaction With DNA ==

The C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box. An important residue in the catalytic site is <scene name='56/566534/Lysine_138/1'>Lys138</scene>

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-06T18:12:04Z

Michele White: /* Protein Function */

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Protein Function ==

NF-Y is a transcription factor (TF), which is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is an important protein involved in histone posttranslational modifications (PTMs) <ref name="mainarticle">PMID: 23332751</ref>. These PTMs aid in regions of the DNA that are destined to be transcribed. NF-Y is also involved in recruiting enzymes responsible for acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications (reference here). Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters.
 NF-Y has two isoforms, which differ in the amount of amino acids in the Q-rich activation domain. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability (reference hereee).
 NF-Y is regulated by redox mechanisms. The regulated subunit has three conserved Cysteines in the A2 helix: C83, C87, and C103; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation(referenceeeee).

== Protein Structure ==

NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA.

== Interaction With DNA ==

The C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box. An important residue in the catalytic site is <scene name='56/566534/Lysine_138/1'>Lys138</scene>

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-06T18:10:04Z

Michele White: /* Protein Function */

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Protein Function ==

NF-Y is a transcription factor (TF), which is a protein that binds to specific DNA sequences, controlling the flow of genetic information from DNA into messenger RNA (mRNA), which leads to the formation of proteins. NF-Y is an important protein involved in histone posttranslational modifications (PTMs) <ref>PMID: 23332751</ref>. These PTMs aid in regions of the DNA that are destined to be transcribed. NF-Y is also involved in recruiting enzymes responsible for acetylations on active promoters, suggesting that NF-Y is involved in switch-modifications (reference here). Furthermore, NF-Y is a sequence-specific TF. It is possible that NF-Y and other sequence-specific TFs determine histone modifications on promoters.
 NF-Y has two isoforms, which differ in the amount of amino acids in the Q-rich activation domain. The purpose of these isoforms has yet to be seen, however studies suggest that certain gene expression is dependent on which isoform is present at a time. Another study showed that NF-YA and NF-YB is required for embryonic stem cell (ESC) viability (reference hereee).
 NF-Y is regulated by redox mechanisms. The regulated subunit has three conserved Cysteines in the A2 helix: C83, C87, and C103; which sense the cellular redox potential and allow heterodimerization under reduced conditions. In oxidized conditions, NF-YB forms heterodimers in the cytoplasm which hinders CCAAT-binding and transcriptional activation(referenceeeee).

== Protein Structure ==

NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB). The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA.

== Interaction With DNA ==

The C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box. An important residue in the catalytic site is <scene name='56/566534/Lysine_138/1'>Lys138</scene>

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-06T15:58:17Z

Michele White: /* Protein Structure */

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Protein Function ==

== Protein Structure ==

NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle">PMID: 23332751</ref>. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle"/>. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the <scene name='56/566534/A1a2_linker/1'>A1A2 linker</scene> segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Interaction With DNA ==

The C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box. An important residue in the catalytic site is <scene name='56/566534/Lysine_138/1'>Lys138</scene>

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-06T15:45:01Z

Michele White:

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Protein Function ==

== Protein Structure ==

NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle">PMID: 23332751</ref>. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle"/>. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the A1A2 linker segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Interaction With DNA ==

The C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box. An important residue in the catalytic site is <scene name='56/566534/Lysine_138/1'>Lys138</scene>

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-06T15:43:08Z

Michele White:

[[Image:4awl.png|left|200px]]
{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Protein Function ==

== Protein Structure ==

NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle">PMID: 23332751</ref>. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle"/>. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the A1A2 linker segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Interaction With DNA ==

The C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box. An important residue in the catalytic site is <scene name='56/566534/Lysine_138/1'>Lys138</scene>

== References ==
<references />

NF-Y Transcription Factor Sandbox

2013-11-06T15:40:06Z

Michele White: /* Protein Structure */

{{STRUCTURE_4awl| PDB=4awl | SCENE= }}

== Protein Function ==

== Protein Structure ==

NF-Y transcription factor consists of <scene name='56/566534/Nf-ya/1'>NF-YA</scene>,
<scene name='56/566534/Nf-yb/1'>NF-YB</scene>, and <scene name='56/566534/Nf-yc/1'>NF-YC</scene> subunits. NF-YA subunit contains two α-helices, NF-YB subunit contains four α-helices and two β-sheets, and NF-YC subunit contains three α-helices and two β-sheets. The NF-YB and NF-YC subunits each contain a histone fold motif and form a NF-YB/NF-YC heterodimer<ref>PMID: 24030830</ref>. One of the two α helices of the NF-YA subunit, the N terminal <scene name='56/566534/Nf-ya_a1_helix/1'>A1 helix</scene>, interacts with NF-YB/NF-YC heterodimer resulting in a heterotrimer. The NF-Y heterotrimer is stabilized by ionic interactions, interactions between the backbone atoms of residues, and hydrophobic residues. Stabilizing ionic interactions occur between Asn239(NF-YA) with Asp109(NF-YC) and Asp112(NF-YC)<ref name="mainarticle">PMID: 23332751</ref>. Residue backbone interactions occur between Leu123(NF-YB) with Phe113(NF-YC), Arg245(NF-YA) with Glu98(NF-YB) and Glu101(NF-YB), Arg249(NF-YA) with Glu90(NF-YB), and Arg250(NF-YA) with Asp116(NF-YC)<ref name="mainarticle"/>. Hydrophobic residues that contribute to the stabilization of the NF-Y heterotrimer are only located at NF-YA and NF-YB subunits at residues Ile246(NF-YA), Phe94(NF-YB), and Ile115(NF-YB)<ref name="mainarticle" />. The NF-Y heterotrimer is also stabilized by the A1A2 linker segment through intramolecular interactions of NF-YA residues on the main chain and side chain. Along with stabilization, the A1A2 linker provides the flexibility needed to direct the NF-YA chain toward DNA<ref name="mainarticle" />.

== Interaction With DNA ==

The C terminal <scene name='56/566534/Nf-ya_a2_helix_in_minor_groo/1'>A2 helix</scene> of the NF-YA subunit inserts deep into the minor groove of DNA. NF-YA A2 helix binds to the <scene name='56/566534/Ccaat_box/4'>CCAAT</scene> box and causes the minor groove to widen at the CCAAT box. An important residue in the catalytic site is <scene name='56/566534/Lysine_138/1'>Lys138</scene>

== References ==
<references />