5x7x - Revision history

OCA at 07:55, 22 November 2023

OCA — Wed, 22 Nov 2023 07:55:28 GMT

←Older revision		Revision as of 07:55, 22 November 2023
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	<StructureSection load='5x7x' size='340' side='right'caption='[[5x7x]], [[Resolution\|resolution]] 2.18Å' scene=''>		<StructureSection load='5x7x' size='340' side='right'caption='[[5x7x]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x7x]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X7X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X7X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x7x]] 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=5X7X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X7X FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.184Å</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=5x7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x7x OCA], [~~http~~://pdbe.org/5x7x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x7x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x7x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x7x ProSAT]</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=5x7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x7x OCA], [https://pdbe.org/5x7x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x7x RCSB], [https://www.ebi.ac.uk/pdbsum/5x7x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x7x 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/H33_HUMAN H33_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: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arimura, Y]]	+	[[Category: Arimura Y]]
-	[[Category: Kurumizaka, H]]	+	[[Category: Kurumizaka H]]
-	[[Category: Taguchi, H]]	+	[[Category: Taguchi H]]
-	~~[[Category: Chromatin]]~~	+
-	~~[[Category: Histone variant]]~~	+
-	~~[[Category: Nucleosome]]~~	+
-	~~[[Category: Structural protein-dna complex~~]]	+

OCA at 07:29, 7 October 2020

OCA — Wed, 07 Oct 2020 07:29:08 GMT

←Older revision		Revision as of 07:29, 7 October 2020
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	==The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution==		==The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution==
-	<StructureSection load='5x7x' size='340' side='right' caption='[[5x7x]], [[Resolution\|resolution]] 2.18Å' scene=''>	+	<StructureSection load='5x7x' size='340' side='right'caption='[[5x7x]], [[Resolution\|resolution]] 2.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x7x]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X7X OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X7X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x7x]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X7X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X7X 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" 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=5x7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x7x OCA], [http://pdbe.org/5x7x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x7x RCSB], [http://www.ebi.ac.uk/pdbsum/5x7x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x7x ProSAT]</span></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=5x7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x7x OCA], [http://pdbe.org/5x7x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x7x RCSB], [http://www.ebi.ac.uk/pdbsum/5x7x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x7x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 5x7x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5x7x" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone 3D structures\|Histone 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Arimura, Y]]		[[Category: Arimura, Y]]
	[[Category: Kurumizaka, H]]		[[Category: Kurumizaka, H]]

OCA at 13:06, 19 April 2017

OCA — Wed, 19 Apr 2017 13:06:25 GMT

←Older revision		Revision as of 13:06, 19 April 2017
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-	'''Unreleased structure'''

-	The ~~entry~~ 5x7x is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution==
		+	<StructureSection load='5x7x' size='340' side='right' caption='[[5x7x]], [[Resolution\|resolution]] 2.18Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5x7x]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X7X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X7X 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>
		+	<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=5x7x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x7x OCA], [http://pdbe.org/5x7x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x7x RCSB], [http://www.ebi.ac.uk/pdbsum/5x7x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x7x 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 ==
		+	Non-allelic histone variants are considered as epigenetic factors that regulate genomic DNA functions in eukaryotic chromosomes. In this study, we identified three new human histone H3 variants (named H3.6, H3.7, and H3.8), which were previously annotated as pseudogenes. H3.6 and H3.8 conserve the H3.3-specific amino acid residues, but H3.7 shares the specific amino acid residues with H3.1. We successfully reconstituted the nucleosome containing H3.6 in vitro and determined its crystal structure. In the H3.6 nucleosome, the H3.6-specific Val62 residue hydrophobically contacts the cognate H4 molecule, but its contact area is smaller than that of the corresponding H3.3 Ile62 residue. The thermal stability assay revealed that the H3.6 nucleosome is substantially unstable, as compared to the H3.3 nucleosome. Interestingly, mutational analysis demonstrated that the H3.6 Val62 residue is fully responsible for the H3.6 nucleosome instability, probably because of the weakened hydrophobic interaction with H4. We also reconstituted the nucleosome containing H3.8, but its thermal stability was quite low. In contrast, purified H3.7 failed to form nucleosomes in vitro. The identification and characterization of these novel human histone H3 variants provide important new insights into understanding the epigenetic regulation of the human genome.

-	~~Authors~~:	+	Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8.,Taguchi H, Xie Y, Horikoshi N, Maehara K, Harada A, Nogami J, Sato K, Arimura Y, Osakabe A, Kujirai T, Iwasaki T, Semba Y, Tachibana T, Kimura H, Ohkawa Y, Kurumizaka H Biochemistry. 2017 Apr 10. doi: 10.1021/acs.biochem.6b01098. PMID:28374988<ref>PMID:28374988</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5x7x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arimura, Y]]
		+	[[Category: Kurumizaka, H]]
		+	[[Category: Taguchi, H]]
		+	[[Category: Chromatin]]
		+	[[Category: Histone variant]]
		+	[[Category: Nucleosome]]
		+	[[Category: Structural protein-dna complex]]

OCA at 12:20, 5 April 2017

OCA — Wed, 05 Apr 2017 12:20:24 GMT

←Older revision		Revision as of 12:20, 5 April 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5x7x is ON HOLD	+	The entry 5x7x is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5x7x" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:52:21 GMT

Protected "5x7x" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:52, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x7x is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Thu, 09 Mar 2017 15:52:20 GMT

New page: '''Unreleased structure''' The entry 5x7x is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5x7x is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]