5b24 - Revision history

OCA at 15:56, 8 November 2023

2023-11-08T15:56:18Z

←Older revision		Revision as of 15:56, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5b24]] 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=5B24 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B24 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b24]] 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=5B24 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B24 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</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]] 3.6Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</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=5b24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b24 OCA], [https://pdbe.org/5b24 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b24 RCSB], [https://www.ebi.ac.uk/pdbsum/5b24 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b24 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=5b24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b24 OCA], [https://pdbe.org/5b24 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b24 RCSB], [https://www.ebi.ac.uk/pdbsum/5b24 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b24 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:36, 31 May 2023

2023-05-31T06:36:10Z

←Older revision		Revision as of 06:36, 31 May 2023
Line 3:		Line 3:
	<StructureSection load='5b24' size='340' side='right'caption='[[5b24]], [[Resolution\|resolution]] 3.60Å' scene=''>		<StructureSection load='5b24' size='340' side='right'caption='[[5b24]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b24]] 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=5B24 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5B24 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b24]] 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=5B24 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B24 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</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=5b24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b24 OCA], [https://pdbe.org/5b24 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b24 RCSB], [https://www.ebi.ac.uk/pdbsum/5b24 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b24 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=5b24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b24 OCA], [~~http~~://pdbe.org/5b24 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5b24 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5b24 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5b24 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 26:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Horikoshi, N]]	+	[[Category: Horikoshi N]]
-	[[Category: Kagawa, W]]	+	[[Category: Kagawa W]]
-	[[Category: Kurumizaka, H]]	+	[[Category: Kurumizaka H]]
-	[[Category: Osakabe, A]]	+	[[Category: Osakabe A]]
-	[[Category: Tachiwana, H]]	+	[[Category: Tachiwana H]]
-	~~[[Category: Cpd]]~~	+
-	~~[[Category: Nucleosome]]~~	+
-	~~[[Category: Photolesion]]~~	+
-	~~[[Category: Structural protein-dna complex~~]]	+

OCA at 10:01, 26 February 2020

2020-02-26T10:01:31Z

←Older revision		Revision as of 10:01, 26 February 2020
Line 1:		Line 1:

	==The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer==		==The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer==
-	<StructureSection load='5b24' size='340' side='right' caption='[[5b24]], [[Resolution\|resolution]] 3.60Å' scene=''>	+	<StructureSection load='5b24' size='340' side='right'caption='[[5b24]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b24]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B24 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B24 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b24]] 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=5B24 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B24 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</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=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</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=5b24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b24 OCA], [http://pdbe.org/5b24 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b24 RCSB], [http://www.ebi.ac.uk/pdbsum/5b24 PDBsum]</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5b24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b24 OCA], [http://pdbe.org/5b24 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b24 RCSB], [http://www.ebi.ac.uk/pdbsum/5b24 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b24 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5b24" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5b24" 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: Horikoshi, N]]		[[Category: Horikoshi, N]]
	[[Category: Kagawa, W]]		[[Category: Kagawa, W]]

OCA at 15:12, 2 March 2016

2016-03-02T15:12:16Z

←Older revision		Revision as of 15:12, 2 March 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5b24 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==The crystal structure of the nucleosome containing cyclobutane pyrimidine dimer==
		+	<StructureSection load='5b24' size='340' side='right' caption='[[5b24]], [[Resolution\|resolution]] 3.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5b24]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B24 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B24 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</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=5b24 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b24 OCA], [http://pdbe.org/5b24 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b24 RCSB], [http://www.ebi.ac.uk/pdbsum/5b24 PDBsum]</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 ==
		+	The cyclobutane pyrimidine dimer (CPD) is induced in genomic DNA by ultraviolet (UV) light. In mammals, this photolesion is primarily induced within nucleosomal DNA, and repaired exclusively by the nucleotide excision repair (NER) pathway. However, the mechanism by which the CPD is accommodated within the nucleosome has remained unknown. We now report the crystal structure of a nucleosome containing CPDs. In the nucleosome, the CPD induces only limited local backbone distortion, and the affected bases are accommodated within the duplex. Interestingly, one of the affected thymine bases is located within 3.0 A from the undamaged complementary adenine base, suggesting the formation of complementary hydrogen bonds in the nucleosome. We also found that UV-DDB, which binds the CPD at the initial stage of the NER pathway, also efficiently binds to the nucleosomal CPD. These results provide important structural and biochemical information for understanding how the CPD is accommodated and recognized in chromatin.

-	~~Authors: Horikoshi~~, N., Tachiwana, H., Kagawa, W., Osakabe, A., ~~Kurumizaka~~, H.	+	Crystal structure of the nucleosome containing ultraviolet light-induced cyclobutane pyrimidine dimer.,Horikoshi N, Tachiwana H, Kagawa W, Osakabe A, Matsumoto S, Iwai S, Sugasawa K, Kurumizaka H Biochem Biophys Res Commun. 2016 Feb 26;471(1):117-22. doi:, 10.1016/j.bbrc.2016.01.170. Epub 2016 Feb 2. PMID:26837048<ref>PMID:26837048</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5b24" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Horikoshi, N]]
		+	[[Category: Kagawa, W]]
	[[Category: Kurumizaka, H]]		[[Category: Kurumizaka, H]]
-	[[Category: Tachiwana, H]]
	[[Category: Osakabe, A]]		[[Category: Osakabe, A]]
-	[[Category: ~~Kagawa~~, W]]	+	[[Category: Tachiwana, H]]
-	[[Category: ~~Horikoshi, N~~]]	+	[[Category: Cpd]]
		+	[[Category: Nucleosome]]
		+	[[Category: Photolesion]]
		+	[[Category: Structural protein-dna complex]]

OCA at 10:07, 3 February 2016

2016-02-03T10:07:47Z

←Older revision		Revision as of 10:07, 3 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5b24 is ON HOLD	+	The entry 5b24 is ON HOLD until Paper Publication

	Authors: Horikoshi, N., Tachiwana, H., Kagawa, W., Osakabe, A., Kurumizaka, H.		Authors: Horikoshi, N., Tachiwana, H., Kagawa, W., Osakabe, A., Kurumizaka, H.

OCA: Protected "5b24" [edit=sysop:move=sysop]

2016-01-13T15:05:18Z

Protected "5b24" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:05, 13 January 2016

OCA: New page: '''Unreleased structure''' The entry 5b24 is ON HOLD Authors: Horikoshi, N., Tachiwana, H., Kagawa, W., Osakabe, A., Kurumizaka, H. Description: Category: Unreleased Structures [[...

2016-01-13T15:05:16Z

New page: '''Unreleased structure''' The entry 5b24 is ON HOLD Authors: Horikoshi, N., Tachiwana, H., Kagawa, W., Osakabe, A., Kurumizaka, H. Description: Category: Unreleased Structures [[...

New page

'''Unreleased structure'''

The entry 5b24 is ON HOLD

Authors: Horikoshi, N., Tachiwana, H., Kagawa, W., Osakabe, A., Kurumizaka, H.

Description:
[[Category: Unreleased Structures]]
[[Category: Kurumizaka, H]]
[[Category: Tachiwana, H]]
[[Category: Osakabe, A]]
[[Category: Kagawa, W]]
[[Category: Horikoshi, N]]