5jrg - Revision history

OCA at 19:03, 20 September 2023

OCA — Wed, 20 Sep 2023 19:03:25 GMT

←Older revision		Revision as of 19:03, 20 September 2023
Line 3:		Line 3:
	<StructureSection load='5jrg' size='340' side='right'caption='[[5jrg]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5jrg' size='340' side='right'caption='[[5jrg]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jrg]] 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=5JRG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JRG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jrg]] 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=5JRG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JRG 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]] 2.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <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'>[https://proteopedia.org/fgij/fg.htm?mol=5jrg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrg OCA], [https://pdbe.org/5jrg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jrg RCSB], [https://www.ebi.ac.uk/pdbsum/5jrg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrg 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=5jrg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrg OCA], [~~http~~://pdbe.org/5jrg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jrg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jrg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrg 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 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arimura, Y]]	+	[[Category: Arimura Y]]
-	[[Category: Horikoshi, N]]	+	[[Category: Horikoshi N]]
-	[[Category: Kurumizaka, H]]	+	[[Category: Kurumizaka H]]
-	[[Category: Osakabe, A]]	+	[[Category: Osakabe A]]
-	~~[[Category: Ap-site]]~~	+
-	~~[[Category: Chromatin formation]]~~	+
-	~~[[Category: Dna binding]]~~	+
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Histone fold]]~~	+
-	~~[[Category: Nucleosome]]~~	+
-	~~[[Category: Nucleus~~]]	+

OCA at 11:35, 17 June 2020

OCA — Wed, 17 Jun 2020 11:35:35 GMT

←Older revision		Revision as of 11:35, 17 June 2020
Line 1:		Line 1:

	==Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF)==		==Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF)==
-	<StructureSection load='5jrg' size='340' side='right' caption='[[5jrg]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5jrg' size='340' side='right'caption='[[5jrg]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jrg]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JRG OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JRG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jrg]] 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=5JRG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JRG 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</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=5jrg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrg OCA], [http://pdbe.org/5jrg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jrg RCSB], [http://www.ebi.ac.uk/pdbsum/5jrg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrg ProSAT]</span></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://proteopedia.org/fgij/fg.htm?mol=5jrg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrg OCA], [http://pdbe.org/5jrg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jrg RCSB], [http://www.ebi.ac.uk/pdbsum/5jrg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5jrg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jrg" 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: Horikoshi, N]]		[[Category: Horikoshi, N]]

OCA at 16:45, 9 March 2017

OCA — Thu, 09 Mar 2017 16:45:21 GMT

←Older revision		Revision as of 16:45, 9 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jrg is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF)==
		+	<StructureSection load='5jrg' size='340' side='right' caption='[[5jrg]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jrg]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JRG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JRG 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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</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=5jrg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jrg OCA], [http://pdbe.org/5jrg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jrg RCSB], [http://www.ebi.ac.uk/pdbsum/5jrg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jrg 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 ==
		+	Huge amounts (>10,000/day) of apurinic/apyrimidinic (AP) sites are produced in genomes, but their structures in chromatin remain undetermined. We determined the crystal structure of the nucleosome containing AP-site analogs at two symmetric sites, which revealed structural polymorphism: one forms an inchworm configuration without an empty space at the AP site, and the other forms a B-form-like structure with an empty space and the orphan base. This unexpected inchworm configuration of the AP site is important to understand the AP DNA repair mechanism, because it may not be recognized by the major AP-binding protein, APE1, during the base excision repair process.

-	~~Authors: Osakabe~~, A., Arimura, Y., ~~Horikoshi~~, N., ~~Kurumizaka~~, H.	+	Polymorphism of apyrimidinic DNA structures in the nucleosome.,Osakabe A, Arimura Y, Matsumoto S, Horikoshi N, Sugasawa K, Kurumizaka H Sci Rep. 2017 Jan 31;7:41783. doi: 10.1038/srep41783. PMID:28139742<ref>PMID:28139742</ref>

-	~~Description: Crystal structure~~ of the ~~nucleosome containing the DNA with tetrahydrofuran (THF)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Kurumizaka, H]]~~	+	<div class="pdbe-citations 5jrg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Arimura, Y]]		[[Category: Arimura, Y]]
-	[[Category: Osakabe, A]]
	[[Category: Horikoshi, N]]		[[Category: Horikoshi, N]]
		+	[[Category: Kurumizaka, H]]
		+	[[Category: Osakabe, A]]
		+	[[Category: Ap-site]]
		+	[[Category: Chromatin formation]]
		+	[[Category: Dna binding]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Histone fold]]
		+	[[Category: Nucleosome]]
		+	[[Category: Nucleus]]

OCA at 12:07, 4 January 2017

OCA — Wed, 04 Jan 2017 12:07:02 GMT

←Older revision		Revision as of 12:07, 4 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Osakabe, A., Arimura, Y., Horikoshi, N., Kurumizaka, H.		Authors: Osakabe, A., Arimura, Y., Horikoshi, N., Kurumizaka, H.

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

OCA — Wed, 01 Jun 2016 13:44:01 GMT

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

←Older revision

Revision as of 13:44, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5jrg is ON HOLD Authors: Osakabe, A., Arimura, Y., Horikoshi, N., Kurumizaka, H. Description: Crystal structure of the nucleosome containing the DN...

OCA — Wed, 01 Jun 2016 13:44:00 GMT

New page: '''Unreleased structure''' The entry 5jrg is ON HOLD Authors: Osakabe, A., Arimura, Y., Horikoshi, N., Kurumizaka, H. Description: Crystal structure of the nucleosome containing the DN...

New page

'''Unreleased structure'''

The entry 5jrg is ON HOLD

Authors: Osakabe, A., Arimura, Y., Horikoshi, N., Kurumizaka, H.

Description: Crystal structure of the nucleosome containing the DNA with tetrahydrofuran (THF)
[[Category: Unreleased Structures]]
[[Category: Kurumizaka, H]]
[[Category: Arimura, Y]]
[[Category: Osakabe, A]]
[[Category: Horikoshi, N]]