5xf5 - Revision history

OCA at 08:01, 22 November 2023

OCA — Wed, 22 Nov 2023 08:01:10 GMT

←Older revision		Revision as of 08:01, 22 November 2023
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	==Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration)==		==Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration)==
-	<StructureSection load='5xf5' size='340' side='right' caption='[[5xf5]], [[Resolution\|resolution]] 2.82Å' scene=''>	+	<StructureSection load='5xf5' size='340' side='right'caption='[[5xf5]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xf5]] 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=5XF5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XF5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xf5]] 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=5XF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XF5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RSK:(1S,2R)-1,2-diphenylethane-1,2-diamine'>RSK</scene>, <scene name='pdbligand=RUD:[ethane6-3-(p-tolyl)propanoic+acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2'>RUD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.82Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xf3\|5xf3]], [[5xf4\|5xf4]], [[5xf6\|5xf6]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RSK:(1S,2R)-1,2-diphenylethane-1,2-diamine'>RSK</scene>, <scene name='pdbligand=RUD:[ethane6-3-(p-tolyl)propanoic+acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2'>RUD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5xf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xf5 OCA], [https://pdbe.org/5xf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xf5 RCSB], [https://www.ebi.ac.uk/pdbsum/5xf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xf5 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=5xf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xf5 OCA], [~~http~~://pdbe.org/5xf5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xf5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xf5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xf5 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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	</div>		</div>
	<div class="pdbe-citations 5xf5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xf5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone 3D structures\|Histone 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Adhireksan, Z~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Davey, C A]]~~	+	[[Category: Adhireksan Z]]
-	~~[[Category: Dyson, P J]]~~	+	[[Category: Davey CA]]
-	~~[[Category: Ma,~~ Z]]	+	[[Category: Dyson PJ]]
-	[[Category: ~~Murray, B S~~]]	+	[[Category: Ma Z]]
-	[[Category: ~~Binuclear metal-based agent~~]]	+	[[Category: Murray BS]]
-	[[Category: ~~Histone adduct~~]]	+
-	[[Category: ~~Nucleosome]]~~	+
-	~~[[Category: Ruthenium compound]]~~	+
-	~~[[Category: Structural protein-dna complex~~]]	+

OCA at 07:55, 6 December 2017

OCA — Wed, 06 Dec 2017 07:55:18 GMT

←Older revision		Revision as of 07:55, 6 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xf5 is ~~ON HOLD~~	+	==Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having a 1,2-diphenylethylenediamine linker (R,S-configuration)==
		+	<StructureSection load='5xf5' size='340' side='right' caption='[[5xf5]], [[Resolution\|resolution]] 2.82Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xf5]] 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=5XF5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XF5 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RSK:(1S,2R)-1,2-diphenylethane-1,2-diamine'>RSK</scene>, <scene name='pdbligand=RUD:[ethane6-3-(p-tolyl)propanoic+acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2'>RUD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xf3\|5xf3]], [[5xf4\|5xf4]], [[5xf6\|5xf6]]</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=5xf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xf5 OCA], [http://pdbe.org/5xf5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xf5 RCSB], [http://www.ebi.ac.uk/pdbsum/5xf5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xf5 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 ==
		+	The 'acidic patch' is a highly electronegative cleft on the histone H2A-H2B dimer in the nucleosome. It is a fundamental motif for protein binding and chromatin dynamics, but the cellular impact of targeting this potentially therapeutic site with exogenous molecules remains unclear. Here, we characterize a family of binuclear ruthenium compounds that selectively target the nucleosome acidic patch, generating intra-nucleosomal H2A-H2B cross-links as well as inter-nucleosomal cross-links. In contrast to cisplatin or the progenitor RAPTA-C anticancer drugs, the binuclear agents neither arrest specific cell cycle phases nor elicit DNA damage response, but rather induce an irreversible, anomalous state of condensed chromatin that ultimately results in apoptosis. In vitro, the compounds induce misfolding of chromatin fibre and block the binding of the regulator of chromatin condensation 1 (RCC1) acidic patch-binding protein. This family of chromatin-modifying molecules has potential for applications in drug development and as tools for chromatin research.

-	~~Authors~~:	+	Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation.,Davey GE, Adhireksan Z, Ma Z, Riedel T, Sharma D, Padavattan S, Rhodes D, Ludwig A, Sandin S, Murray BS, Dyson PJ, Davey CA Nat Commun. 2017 Nov 17;8(1):1575. doi: 10.1038/s41467-017-01680-4. PMID:29146919<ref>PMID:29146919</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xf5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Adhireksan, Z]]
		+	[[Category: Davey, C A]]
		+	[[Category: Dyson, P J]]
		+	[[Category: Ma, Z]]
		+	[[Category: Murray, B S]]
		+	[[Category: Binuclear metal-based agent]]
		+	[[Category: Histone adduct]]
		+	[[Category: Nucleosome]]
		+	[[Category: Ruthenium compound]]
		+	[[Category: Structural protein-dna complex]]

OCA: Protected "5xf5" [edit=sysop:move=sysop]

OCA — Wed, 19 Apr 2017 12:07:02 GMT

Protected "5xf5" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:07, 19 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xf5 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Apr 2017 12:07:00 GMT

New page: '''Unreleased structure''' The entry 5xf5 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5xf5 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]