5ay8: Difference between revisions
New page: '''Unreleased structure''' The entry 5ay8 is ON HOLD Authors: Kujirai, T., Horikoshi, N., Sato, K., Maehara, K., Machida, S., Osakabe, A., Kimura, H., Ohkawa, Y., Kurumizaka, H. Descri... |
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==Crystal structure of human nucleosome containing H3.Y== | |||
<StructureSection load='5ay8' size='340' side='right'caption='[[5ay8]], [[Resolution|resolution]] 2.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5ay8]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AY8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AY8 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ay8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ay8 OCA], [https://pdbe.org/5ay8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ay8 RCSB], [https://www.ebi.ac.uk/pdbsum/5ay8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ay8 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/H3Y1_HUMAN H3Y1_HUMAN] Primate-specific variant histone H3, which constitutes a core component of nucleosomes (PubMed:20819935, PubMed:27016736). Histone H3.Y-containing nucleosomes accumulate around transcription start sites and have flexible DNA ends, suggesting that they form relaxed chromatin that allows transcription factor access (PubMed:27016736). Histone H1 binds less efficiently to histone H3.Y-containing nucleosomes (PubMed:27016736). Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling (Probable).<ref>PMID:20819935</ref> <ref>PMID:27016736</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Histone H3.Y is a primate-specific, distant H3 variant. It is evolutionarily derived from H3.3, and may function in transcription regulation. However, the mechanism by which H3.Y regulates transcription has not been elucidated. In the present study, we determined the crystal structure of the H3.Y nucleosome, and found that many H3.Y-specific residues are located on the entry/exit sites of the nucleosome. Biochemical analyses revealed that the DNA ends of the H3.Y nucleosome were more flexible than those of the H3.3 nucleosome, although the H3.Y nucleosome was stablein vitroandin vivo Interestingly, the linker histone H1, which compacts nucleosomal DNA, appears to bind to the H3.Y nucleosome less efficiently, as compared to the H3.3 nucleosome. These characteristics of the H3.Y nucleosome are also conserved in the H3.Y/H3.3 heterotypic nucleosome, which may be the predominant form in cells. In human cells, H3.Y preferentially accumulated around transcription start sites (TSSs). Taken together, H3.Y-containing nucleosomes around transcription start sites may form relaxed chromatin that allows transcription factor access, to regulate the transcription status of specific genes. | |||
Structure and function of human histone H3.Y nucleosome.,Kujirai T, Horikoshi N, Sato K, Maehara K, Machida S, Osakabe A, Kimura H, Ohkawa Y, Kurumizaka H Nucleic Acids Res. 2016 Mar 25. pii: gkw202. PMID:27016736<ref>PMID:27016736</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5ay8" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Histone 3D structures|Histone 3D structures]] | ||
[[Category: | == References == | ||
[[Category: Machida | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: Osakabe | </StructureSection> | ||
[[Category: | [[Category: Homo sapiens]] | ||
[[Category: Large Structures]] | |||
[[Category: Horikoshi N]] | |||
[[Category: Kimura H]] | |||
[[Category: Kujirai T]] | |||
[[Category: Kurumizaka H]] | |||
[[Category: Machida S]] | |||
[[Category: Maehara K]] | |||
[[Category: Ohkawa Y]] | |||
[[Category: Osakabe A]] | |||
[[Category: Sato K]] | |||
Latest revision as of 18:51, 8 November 2023
Crystal structure of human nucleosome containing H3.YCrystal structure of human nucleosome containing H3.Y
Structural highlights
FunctionH3Y1_HUMAN Primate-specific variant histone H3, which constitutes a core component of nucleosomes (PubMed:20819935, PubMed:27016736). Histone H3.Y-containing nucleosomes accumulate around transcription start sites and have flexible DNA ends, suggesting that they form relaxed chromatin that allows transcription factor access (PubMed:27016736). Histone H1 binds less efficiently to histone H3.Y-containing nucleosomes (PubMed:27016736). Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling (Probable).[1] [2] Publication Abstract from PubMedHistone H3.Y is a primate-specific, distant H3 variant. It is evolutionarily derived from H3.3, and may function in transcription regulation. However, the mechanism by which H3.Y regulates transcription has not been elucidated. In the present study, we determined the crystal structure of the H3.Y nucleosome, and found that many H3.Y-specific residues are located on the entry/exit sites of the nucleosome. Biochemical analyses revealed that the DNA ends of the H3.Y nucleosome were more flexible than those of the H3.3 nucleosome, although the H3.Y nucleosome was stablein vitroandin vivo Interestingly, the linker histone H1, which compacts nucleosomal DNA, appears to bind to the H3.Y nucleosome less efficiently, as compared to the H3.3 nucleosome. These characteristics of the H3.Y nucleosome are also conserved in the H3.Y/H3.3 heterotypic nucleosome, which may be the predominant form in cells. In human cells, H3.Y preferentially accumulated around transcription start sites (TSSs). Taken together, H3.Y-containing nucleosomes around transcription start sites may form relaxed chromatin that allows transcription factor access, to regulate the transcription status of specific genes. Structure and function of human histone H3.Y nucleosome.,Kujirai T, Horikoshi N, Sato K, Maehara K, Machida S, Osakabe A, Kimura H, Ohkawa Y, Kurumizaka H Nucleic Acids Res. 2016 Mar 25. pii: gkw202. PMID:27016736[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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