5cpj - Revision history

OCA at 16:11, 8 November 2023

2023-11-08T16:11:06Z

←Older revision		Revision as of 16:11, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5cpj]] 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=5CPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CPJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5cpj]] 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=5CPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CPJ FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.15Å</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'>[https://proteopedia.org/fgij/fg.htm?mol=5cpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cpj OCA], [https://pdbe.org/5cpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cpj RCSB], [https://www.ebi.ac.uk/pdbsum/5cpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cpj 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=5cpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cpj OCA], [https://pdbe.org/5cpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cpj RCSB], [https://www.ebi.ac.uk/pdbsum/5cpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cpj ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:22, 14 June 2023

2023-06-14T12:22:14Z

←Older revision		Revision as of 12:22, 14 June 2023
Line 3:		Line 3:
	<StructureSection load='5cpj' size='340' side='right'caption='[[5cpj]], [[Resolution\|resolution]] 3.15Å' scene=''>		<StructureSection load='5cpj' size='340' side='right'caption='[[5cpj]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5cpj]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CPJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5CPJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5cpj]] 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=5CPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CPJ 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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cpi\|5cpi]], [[5cpk\|5cpk]]</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=5cpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cpj OCA], [https://pdbe.org/5cpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cpj RCSB], [https://www.ebi.ac.uk/pdbsum/5cpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cpj 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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5cpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cpj OCA], [~~http~~://pdbe.org/5cpj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5cpj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5cpj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5cpj 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 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Adachi, F]]	+	[[Category: Adachi F]]
-	[[Category: Arimura, Y]]	+	[[Category: Arimura Y]]
-	[[Category: Kurumizaka, H]]	+	[[Category: Kurumizaka H]]
-	[[Category: Maehara, K]]	+	[[Category: Maehara K]]
-	[[Category: Ohkawa, Y]]	+	[[Category: Ohkawa Y]]
-	[[Category: Osakabe, A]]	+	[[Category: Osakabe A]]
-	~~[[Category: Structural protein-dna complex]]~~	+
-	~~[[Category: Chromatin formation]]~~	+
-	~~[[Category: Dna binding]]~~	+
-	~~[[Category: Dna methylation]]~~	+
-	~~[[Category: Histone fold]]~~	+
-	~~[[Category: Nucleosome]]~~	+
-	~~[[Category: Nucleus~~]]	+

OCA at 07:10, 19 February 2020

2020-02-19T07:10:27Z

←Older revision		Revision as of 07:10, 19 February 2020
Line 1:		Line 1:

	==Nucleosome containing methylated Sat2R DNA==		==Nucleosome containing methylated Sat2R DNA==
-	<StructureSection load='5cpj' size='340' side='right' caption='[[5cpj]], [[Resolution\|resolution]] 3.15Å' scene=''>	+	<StructureSection load='5cpj' size='340' side='right'caption='[[5cpj]], [[Resolution\|resolution]] 3.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5cpj]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CPJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5cpj]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CPJ 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cpi\|5cpi]], [[5cpk\|5cpk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cpi\|5cpi]], [[5cpk\|5cpk]]</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=5cpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cpj OCA], [http://pdbe.org/5cpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cpj RCSB], [http://www.ebi.ac.uk/pdbsum/5cpj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cpj 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=5cpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cpj OCA], [http://pdbe.org/5cpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cpj RCSB], [http://www.ebi.ac.uk/pdbsum/5cpj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cpj ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:

	==See Also==		==See Also==
-	*[[Histone\|Histone]]	+	*[[Histone 3D structures\|Histone 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Adachi, F]]		[[Category: Adachi, F]]
	[[Category: Arimura, Y]]		[[Category: Arimura, Y]]

OCA at 17:12, 18 August 2017

2017-08-18T17:12:31Z

←Older revision		Revision as of 17:12, 18 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5cpj is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Nucleosome containing methylated Sat2R DNA==
		+	<StructureSection load='5cpj' size='340' side='right' caption='[[5cpj]], [[Resolution\|resolution]] 3.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5cpj]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CPJ 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5cpi\|5cpi]], [[5cpk\|5cpk]]</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=5cpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cpj OCA], [http://pdbe.org/5cpj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cpj RCSB], [http://www.ebi.ac.uk/pdbsum/5cpj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cpj 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 ==
		+	DNA methylation occurs on CpG sites and is important to form pericentric heterochromatin domains. The satellite 2 sequence, containing seven CpG sites, is located in the pericentric region of human chromosome 1 and is highly methylated in normal cells. In contrast, the satellite 2 region is reportedly hypomethylated in cancer cells, suggesting that the methylation status may affect the chromatin structure around the pericentric regions in tumours. In this study, we mapped the nucleosome positioning on the satellite 2 sequence in vitro and found that DNA methylation modestly affects the distribution of the nucleosome positioning. The micrococcal nuclease assay revealed that the DNA end flexibility of the nucleosomes changes, depending on the DNA methylation status. However, the structures and thermal stabilities of the nucleosomes are unaffected by DNA methylation. These findings provide new information to understand how DNA methylation functions in regulating pericentric heterochromatin formation and maintenance in normal and malignant cells.

-	~~Authors: Osakabe~~, A., Arimura, Y~~., Adachi, F.~~, Maehara, K., Ohkawa, Y., Kurumizaka, H.	+	Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA.,Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H Open Biol. 2015 Oct;5(10). pii: 150128. doi: 10.1098/rsob.150128. PMID:26446621<ref>PMID:26446621</ref>

-	~~Description:~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Ohkawa, Y]]~~	+	<div class="pdbe-citations 5cpj" style="background-color:#fffaf0;"></div>
-	~~[[Category: Maehara, K]]~~	+
-	[[~~Category: Kurumizaka, H~~]]	+	==See Also==
-	~~[[Category: Arimura, Y]]~~	+	*[[Histone\|Histone]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Adachi, F]]		[[Category: Adachi, F]]
		+	[[Category: Arimura, Y]]
		+	[[Category: Kurumizaka, H]]
		+	[[Category: Maehara, K]]
		+	[[Category: Ohkawa, Y]]
	[[Category: Osakabe, A]]		[[Category: Osakabe, A]]
		+	[[Category: Structural protein-dna complex]]
		+	[[Category: Chromatin formation]]
		+	[[Category: Dna binding]]
		+	[[Category: Dna methylation]]
		+	[[Category: Histone fold]]
		+	[[Category: Nucleosome]]
		+	[[Category: Nucleus]]

OCA at 10:50, 2 September 2015

2015-09-02T10:50:19Z

←Older revision		Revision as of 10:50, 2 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Osakabe, A., Arimura, Y., Adachi, F., Maehara, K., Ohkawa, Y., Kurumizaka, H.		Authors: Osakabe, A., Arimura, Y., Adachi, F., Maehara, K., Ohkawa, Y., Kurumizaka, H.

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

2015-07-29T13:41:46Z

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

←Older revision

Revision as of 13:41, 29 July 2015

OCA: New page: '''Unreleased structure''' The entry 5cpj is ON HOLD Authors: Osakabe, A., Arimura, Y., Adachi, F., Maehara, K., Ohkawa, Y., Kurumizaka, H. Description: [[Category: Unreleased Structu...

2015-07-29T13:41:45Z

New page: '''Unreleased structure''' The entry 5cpj is ON HOLD Authors: Osakabe, A., Arimura, Y., Adachi, F., Maehara, K., Ohkawa, Y., Kurumizaka, H. Description: [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 5cpj is ON HOLD

Authors: Osakabe, A., Arimura, Y., Adachi, F., Maehara, K., Ohkawa, Y., Kurumizaka, H.

Description:
[[Category: Unreleased Structures]]
[[Category: Ohkawa, Y]]
[[Category: Maehara, K]]
[[Category: Kurumizaka, H]]
[[Category: Arimura, Y]]
[[Category: Adachi, F]]
[[Category: Osakabe, A]]