5gse - Revision history

OCA at 11:41, 2 August 2023

OCA — Wed, 02 Aug 2023 11:41:05 GMT

←Older revision		Revision as of 11:41, 2 August 2023
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	<StructureSection load='5gse' size='340' side='right'caption='[[5gse]], [[Resolution\|resolution]] 3.14Å' scene=''>		<StructureSection load='5gse' size='340' side='right'caption='[[5gse]], [[Resolution\|resolution]] 3.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gse]] is a 16 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=5GSE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5GSE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gse]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GSE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GSE FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=5CM:5~~-~~METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</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]] 3.14Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>HIST1H3A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN]), HIST1H4A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN]), HIST1H2AB ([http~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5~~&id=9606 HUMAN]), HIST1H2BJ ([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=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5gse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gse OCA], [~~http~~://pdbe.org/5gse PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5gse RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5gse PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5gse 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=5gse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gse OCA], [https://pdbe.org/5gse PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gse RCSB], [https://www.ebi.ac.uk/pdbsum/5gse PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gse 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 ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arimura, Y]]	+	[[Category: Synthetic construct]]
-	[[Category: Kato, D]]	+	[[Category: Arimura Y]]
-	[[Category: Kurumizaka, H]]	+	[[Category: Kato D]]
-	[[Category: Osakabe, A]]	+	[[Category: Kurumizaka H]]
-	[[Category: Park~~, S Y]]~~	+	[[Category: Osakabe A]]
-	~~[[Category: Dna-binding]]~~	+	[[Category: Park SY]]
-	~~[[Category: Histone-fold]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Structural protein-dna complex~~]]	+

OCA at 06:42, 20 May 2020

OCA — Wed, 20 May 2020 06:42:46 GMT

←Older revision		Revision as of 06:42, 20 May 2020
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	==Crystal structure of unusual nucleosome==		==Crystal structure of unusual nucleosome==
-	<StructureSection load='5gse' size='340' side='right' caption='[[5gse]], [[Resolution\|resolution]] 3.14Å' scene=''>	+	<StructureSection load='5gse' size='340' side='right'caption='[[5gse]], [[Resolution\|resolution]] 3.14Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5gse]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GSE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5GSE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5gse]] is a 16 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=5GSE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5GSE FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</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=5gse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gse OCA], [http://pdbe.org/5gse PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gse RCSB], [http://www.ebi.ac.uk/pdbsum/5gse PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gse ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HIST1H3A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H4A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H2AB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), HIST1H2BJ ([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://proteopedia.org/fgij/fg.htm?mol=5gse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gse OCA], [http://pdbe.org/5gse PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gse RCSB], [http://www.ebi.ac.uk/pdbsum/5gse PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gse ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5gse" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5gse" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone 3D structures\|Histone 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arimura, Y]]		[[Category: Arimura, Y]]
	[[Category: Kato, D]]		[[Category: Kato, D]]

OCA at 13:00, 4 May 2017

OCA — Thu, 04 May 2017 13:00:30 GMT

←Older revision		Revision as of 13:00, 4 May 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5gse is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of unusual nucleosome==
		+	<StructureSection load='5gse' size='340' side='right' caption='[[5gse]], [[Resolution\|resolution]] 3.14Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5gse]] is a 16 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GSE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GSE FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</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=5gse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gse OCA], [http://pdbe.org/5gse PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gse RCSB], [http://www.ebi.ac.uk/pdbsum/5gse PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gse 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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nucleosomes are dynamic entities that are repositioned along DNA by chromatin remodeling processes. A nucleosome repositioned by the switch-sucrose nonfermentable (SWI/SNF) remodeler collides with a neighbor and forms the intermediate "overlapping dinucleosome." Here, we report the crystal structure of the overlapping dinucleosome, in which two nucleosomes are associated, at 3.14-angstrom resolution. In the overlapping dinucleosome structure, the unusual "hexasome" nucleosome, composed of the histone hexamer lacking one H2A-H2B dimer from the conventional histone octamer, contacts the canonical "octasome" nucleosome, and they intimately associate. Consequently, about 250 base pairs of DNA are left-handedly wrapped in three turns, without a linker DNA segment between the hexasome and octasome moieties. The overlapping dinucleosome structure may provide important information to understand how nucleosome repositioning occurs during the chromatin remodeling process.

-	~~Authors~~:	+	Crystal structure of the overlapping dinucleosome composed of hexasome and octasome.,Kato D, Osakabe A, Arimura Y, Mizukami Y, Horikoshi N, Saikusa K, Akashi S, Nishimura Y, Park SY, Nogami J, Maehara K, Ohkawa Y, Matsumoto A, Kono H, Inoue R, Sugiyama M, Kurumizaka H Science. 2017 Apr 14;356(6334):205-208. doi: 10.1126/science.aak9867. PMID:28408607<ref>PMID:28408607</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5gse" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arimura, Y]]
		+	[[Category: Kato, D]]
		+	[[Category: Kurumizaka, H]]
		+	[[Category: Osakabe, A]]
		+	[[Category: Park, S Y]]
		+	[[Category: Dna-binding]]
		+	[[Category: Histone-fold]]
		+	[[Category: Nucleus]]
		+	[[Category: Structural protein-dna complex]]

OCA at 09:05, 9 March 2017

OCA — Thu, 09 Mar 2017 09:05:30 GMT

←Older revision		Revision as of 09:05, 9 March 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

OCA at 11:57, 1 February 2017

OCA — Wed, 01 Feb 2017 11:57:33 GMT

←Older revision		Revision as of 11:57, 1 February 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5gse is ON HOLD ~~until Paper Publication~~	+	The entry 5gse is ON HOLD

	Authors:		Authors:

OCA at 10:26, 14 September 2016

OCA — Wed, 14 Sep 2016 10:26:02 GMT

←Older revision		Revision as of 10:26, 14 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Fri, 09 Sep 2016 12:01:22 GMT

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

←Older revision

Revision as of 12:01, 9 September 2016

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

OCA — Fri, 09 Sep 2016 12:01:21 GMT

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

New page

'''Unreleased structure'''

The entry 5gse is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]