5ay8

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of human nucleosome containing H3.Y

Structural highlights

5ay8 is a 10 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2]

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^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wiedemann SM, Mildner SN, Bönisch C, Israel L, Maiser A, Matheisl S, Straub T, Merkl R, Leonhardt H, Kremmer E, Schermelleh L, Hake SB. Identification and characterization of two novel primate-specific histone H3 variants, H3.X and H3.Y. J Cell Biol. 2010 Sep 6;190(5):777-91. PMID:20819935 doi:10.1083/jcb.201002043
↑ Kujirai T, Horikoshi N, Sato K, Maehara K, Machida S, Osakabe A, Kimura H, Ohkawa Y, Kurumizaka H. Structure and function of human histone H3.Y nucleosome. Nucleic Acids Res. 2016 Mar 25. pii: gkw202. PMID:27016736 doi:http://dx.doi.org/10.1093/nar/gkw202
↑ Kujirai T, Horikoshi N, Sato K, Maehara K, Machida S, Osakabe A, Kimura H, Ohkawa Y, Kurumizaka H. Structure and function of human histone H3.Y nucleosome. Nucleic Acids Res. 2016 Mar 25. pii: gkw202. PMID:27016736 doi:http://dx.doi.org/10.1093/nar/gkw202

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5ay8"

@@ Line 1: / Line 1: @@
 ==Crystal structure of human nucleosome containing H3.Y==
-<StructureSection load='5ay8' size='340' side='right' caption='[[5ay8]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+<StructureSection load='5ay8' size='340' side='right'caption='[[5ay8]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ay8]] is a 10 chain structure. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AY8 FirstGlance]. <br>
+<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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ay8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ay8 OCA], [http://pdbe.org/5ay8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ay8 RCSB], [http://www.ebi.ac.uk/pdbsum/5ay8 PDBsum]</span></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 ==
-[[http://www.uniprot.org/uniprot/H2B1J_HUMAN H2B1J_HUMAN]] Core component of nucleosome. 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.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref>   Has broad antibacterial activity. May contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.<ref>PMID:11859126</ref> <ref>PMID:12860195</ref> <ref>PMID:15019208</ref>
+[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 ==
@@ Line 18: / Line 19: @@
 </div>
 <div class="pdbe-citations 5ay8" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Histone 3D structures|Histone 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Horikoshi, N]]
+[[Category: Homo sapiens]]
-[[Category: Kimura, H]]
+[[Category: Large Structures]]
-[[Category: Kujirai, T]]
+[[Category: Horikoshi N]]
-[[Category: Kurumizaka, H]]
+[[Category: Kimura H]]
-[[Category: Machida, S]]
+[[Category: Kujirai T]]
-[[Category: Maehara, K]]
+[[Category: Kurumizaka H]]
-[[Category: Ohkawa, Y]]
+[[Category: Machida S]]
-[[Category: Osakabe, A]]
+[[Category: Maehara K]]
-[[Category: Sato, K]]
+[[Category: Ohkawa Y]]
-[[Category: Dna binding protein-dna complex]]
+[[Category: Osakabe A]]
-[[Category: Histone fold dna binding nucleus]]
+[[Category: Sato K]]

5ay8

From Proteopedia

Current revision

Crystal structure of human nucleosome containing H3.Y

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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