5y0d - Revision history

OCA at 08:18, 22 November 2023

OCA — Wed, 22 Nov 2023 08:18:26 GMT

←Older revision		Revision as of 08:18, 22 November 2023
Line 1:		Line 1:

	==Crystal Structure of the human nucleosome containing the H2B E76K mutant==		==Crystal Structure of the human nucleosome containing the H2B E76K mutant==
-	<StructureSection load='5y0d' size='340' side='right' caption='[[5y0d]], [[Resolution\|resolution]] 1.99Å' scene=''>	+	<StructureSection load='5y0d' size='340' side='right'caption='[[5y0d]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y0d]] is a 10 chain structure with sequence from [~~http://en.wikipedia.org/wiki/ ] and [http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y0D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y0d]] 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=5Y0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y0D 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]] 1.99Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=~~Info&srchmode~~=~~5&id=9606 HUMAN]), HIST1H4A, H4~~/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=~~Info&srchmode~~=~~5&id=9606 HUMAN]), HIST1H2AB, H2AFM, HIST1H2AE, H2AFA~~ (~~[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]~~)~~, HIST1H2BJ, H2BFR ([http:~~/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5y0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0d OCA], [~~http~~://pdbe.org/5y0d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y0d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y0d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0d ProSAT]</span></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=5y0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0d OCA], [https://pdbe.org/5y0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y0d RCSB], [https://www.ebi.ac.uk/pdbsum/5y0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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/H31_HUMAN H31_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5y0d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5y0d" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone 3D structures\|Histone 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: Arimura, Y]]	+	[[Category: Large Structures]]
-	[[Category: Fujita, R]]	+	[[Category: Arimura Y]]
-	[[Category: Kurumizaka, H]]	+	[[Category: Fujita R]]
-	[[Category: Noda, M]]	+	[[Category: Kurumizaka H]]
-	~~[[Category: Chromatin formation]]~~	+	[[Category: Noda M]]
-	~~[[Category: Dna binding]]~~	+
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Histone fold]]~~	+
-	~~[[Category: Nucleosome]]~~	+
-	~~[[Category: Nucleus~~]]	+

OCA at 07:52, 29 August 2018

OCA — Wed, 29 Aug 2018 07:52:37 GMT

←Older revision		Revision as of 07:52, 29 August 2018
Line 3:		Line 3:
	<StructureSection load='5y0d' size='340' side='right' caption='[[5y0d]], [[Resolution\|resolution]] 1.99Å' scene=''>		<StructureSection load='5y0d' size='340' side='right' caption='[[5y0d]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y0d]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y0D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y0d]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y0D 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='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>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIST1H3A, H3FA, HIST1H3B, H3FL, HIST1H3C, H3FC, HIST1H3D, H3FB, HIST1H3E, H3FD, HIST1H3F, H3FI, HIST1H3G, H3FH, HIST1H3H, H3FK, HIST1H3I, H3FF, HIST1H3J, H3FJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H2AB, H2AFM, HIST1H2AE, H2AFA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H2BJ, H2BFR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5y0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0d OCA], [http://pdbe.org/5y0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0d RCSB], [http://www.ebi.ac.uk/pdbsum/5y0d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0d ProSAT]</span></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=5y0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0d OCA], [http://pdbe.org/5y0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0d RCSB], [http://www.ebi.ac.uk/pdbsum/5y0d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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>		[[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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mutations of the Glu76 residue of canonical histone H2B are frequently found in cancer cells. However, it is quite mysterious how a single amino acid substitution in one of the multiple H2B genes affects cell fate. Here we found that the H2B E76K mutation, in which Glu76 is replaced by Lys (E76K), distorted the interface between H2B and H4 in the nucleosome, as revealed by the crystal structure and induced nucleosome instability in vivo and in vitro. Exogenous production of the H2B E76K mutant robustly enhanced the colony formation ability of the expressing cells, indicating that the H2B E76K mutant has the potential to promote oncogenic transformation in the presence of wild-type H2B. We found that other cancer-associated mutations of histones, H3.1 E97K and H2A.Z.1 R80C, also induced nucleosome instability. Interestingly, like the H2B E76K mutant, the H3.1 E97K mutant was minimally incorporated into chromatin in cells, but it enhanced the colony formation ability. In contrast, the H2A.Z.1 R80C mutant was incorporated into chromatin in cells, and had minor effects on the colony formation ability of the cells. These characteristics of histones with cancer-associated mutations may provide important information toward understanding how the mutations promote cancer progression.
		+
		+	Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome.,Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W, Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H Nucleic Acids Res. 2018 Jul 24. pii: 5057090. doi: 10.1093/nar/gky661. PMID:30053102<ref>PMID:30053102</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5y0d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Arimura, Y]]		[[Category: Arimura, Y]]
	[[Category: Fujita, R]]		[[Category: Fujita, R]]

OCA at 07:29, 18 July 2018

OCA — Wed, 18 Jul 2018 07:29:56 GMT

←Older revision		Revision as of 07:29, 18 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5y0d is ~~ON HOLD~~ ~~until Jan 16 2020~~	+	==Crystal Structure of the human nucleosome containing the H2B E76K mutant==
-		+	<StructureSection load='5y0d' size='340' side='right' caption='[[5y0d]], [[Resolution\|resolution]] 1.99Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5y0d]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y0D FirstGlance]. <br>
-	~~Description~~:	+	</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>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5y0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y0d OCA], [http://pdbe.org/5y0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y0d RCSB], [http://www.ebi.ac.uk/pdbsum/5y0d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y0d 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>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arimura, Y]]
		+	[[Category: Fujita, R]]
		+	[[Category: Kurumizaka, H]]
		+	[[Category: Noda, M]]
		+	[[Category: Chromatin formation]]
		+	[[Category: Dna binding]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Histone fold]]
		+	[[Category: Nucleosome]]
		+	[[Category: Nucleus]]

OCA at 03:47, 20 June 2018

OCA — Wed, 20 Jun 2018 03:47:43 GMT

←Older revision		Revision as of 03:47, 20 June 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5y0d is ON HOLD until ~~Paper Publication~~	+	The entry 5y0d is ON HOLD until Jan 16 2020

	Authors:		Authors:

OCA at 07:02, 10 January 2018

OCA — Wed, 10 Jan 2018 07:02:09 GMT

←Older revision		Revision as of 07:02, 10 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5y0d is ON HOLD	+	The entry 5y0d is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5y0d" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 15:59:45 GMT

Protected "5y0d" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:59, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y0d is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 15:59:44 GMT

New page: '''Unreleased structure''' The entry 5y0d is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5y0d is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]