5xf6 - Revision history

OCA at 08:01, 22 November 2023

OCA — Wed, 22 Nov 2023 08:01:11 GMT

←Older revision		Revision as of 08:01, 22 November 2023
Line 1:		Line 1:

	==Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker==		==Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker==
-	<StructureSection load='5xf6' size='340' side='right' caption='[[5xf6]], [[Resolution\|resolution]] 2.63Å' scene=''>	+	<StructureSection load='5xf6' size='340' side='right'caption='[[5xf6]], [[Resolution\|resolution]] 2.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xf6]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~African_clawed_frog African clawed frog~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XF6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XF6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xf6]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XF6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XF6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDN:ETHANE-1,2-DIAMINE'>EDN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.63Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xf3\|5xf3]], [[5xf4\|5xf4]], [[5xf5\|5xf5]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDN:ETHANE-1,2-DIAMINE'>EDN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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">hist1h2aj, LOC494591 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog])</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=5xf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xf6 OCA], [https://pdbe.org/5xf6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xf6 RCSB], [https://www.ebi.ac.uk/pdbsum/5xf6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xf6 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=5xf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xf6 OCA], [~~http~~://pdbe.org/5xf6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xf6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xf6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xf6 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/H2B11_XENLA H2B11_XENLA]] 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. [[http://www.uniprot.org/uniprot/H32_XENLA H32_XENLA]] 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. [[http://www.uniprot.org/uniprot/H4_XENLA H4_XENLA]] 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.	+	[https://www.uniprot.org/uniprot/H32_XENLA H32_XENLA] 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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5xf6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xf6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Histone 3D structures\|Histone 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~African clawed frog~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Adhireksan, Z~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Davey, C A~~]]	+	[[Category: Xenopus laevis]]
-	[[Category: ~~Dyson, P J]]~~	+	[[Category: Adhireksan Z]]
-	~~[[Category: Ma,~~ Z]]	+	[[Category: Davey CA]]
-	[[Category: ~~Murray, B S~~]]	+	[[Category: Dyson PJ]]
-	[[Category: ~~Binuclear metal-based agent~~]]	+	[[Category: Ma Z]]
-	[[Category: ~~Histone adduct~~]]	+	[[Category: Murray BS]]
-	[[Category: ~~Nucleosome]]~~	+
-	~~[[Category: Ruthenium compound]]~~	+
-	~~[[Category: Structural protein-dna complex~~]]	+

OCA at 07:55, 6 December 2017

OCA — Wed, 06 Dec 2017 07:55:30 GMT

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

-	~~The entry~~ 5xf6 is ~~ON HOLD~~	+	==Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker==
		+	<StructureSection load='5xf6' size='340' side='right' caption='[[5xf6]], [[Resolution\|resolution]] 2.63Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xf6]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XF6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XF6 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDN:ETHANE-1,2-DIAMINE'>EDN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]], [[5xf5\|5xf5]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">hist1h2aj, LOC494591 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog])</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=5xf6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xf6 OCA], [http://pdbe.org/5xf6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xf6 RCSB], [http://www.ebi.ac.uk/pdbsum/5xf6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xf6 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/H2B11_XENLA H2B11_XENLA]] 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. [[http://www.uniprot.org/uniprot/H32_XENLA H32_XENLA]] 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. [[http://www.uniprot.org/uniprot/H4_XENLA H4_XENLA]] 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.
		+	<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: Ma, Z~~., Adhireksan, Z., ~~Murray~~, B.S., Dyson, P.J.~~, Davey, C~~.A.	+	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: Nucleosome core particle with an adduct of~~ a ~~binuclear RAPTA (Ru~~-~~arene~~-~~phosphaadamantane) compound having an ethylenediamine linker~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xf6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: African clawed frog]]
	[[Category: Adhireksan, Z]]		[[Category: Adhireksan, Z]]
-	[[Category: Davey, C.A]]	+	[[Category: Davey, C A]]
-	[[Category: ~~Murray~~, ~~B.S~~]]	+	[[Category: Dyson, P J]]
	[[Category: Ma, Z]]		[[Category: Ma, Z]]
-	[[Category: ~~Dyson~~, ~~P.J~~]]	+	[[Category: Murray, B S]]
		+	[[Category: Binuclear metal-based agent]]
		+	[[Category: Histone adduct]]
		+	[[Category: Nucleosome]]
		+	[[Category: Ruthenium compound]]
		+	[[Category: Structural protein-dna complex]]

OCA at 15:26, 27 September 2017

OCA — Wed, 27 Sep 2017 15:26:11 GMT

←Older revision		Revision as of 15:26, 27 September 2017
Line 7:		Line 7:
	Description: Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker		Description: Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Dyson, P.J]]
	[[Category: Adhireksan, Z]]		[[Category: Adhireksan, Z]]
	[[Category: Davey, C.A]]		[[Category: Davey, C.A]]
	[[Category: Murray, B.S]]		[[Category: Murray, B.S]]
	[[Category: Ma, Z]]		[[Category: Ma, Z]]
		+	[[Category: Dyson, P.J]]

OCA: Protected "5xf6" [edit=sysop:move=sysop]

OCA — Wed, 19 Apr 2017 12:07:05 GMT

Protected "5xf6" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:07, 19 April 2017

OCA: New page: '''Unreleased structure''' The entry 5xf6 is ON HOLD Authors: Ma, Z., Adhireksan, Z., Murray, B.S., Dyson, P.J., Davey, C.A. Description: Nucleosome core particle with an adduct of a b...

OCA — Wed, 19 Apr 2017 12:07:03 GMT

New page: '''Unreleased structure''' The entry 5xf6 is ON HOLD Authors: Ma, Z., Adhireksan, Z., Murray, B.S., Dyson, P.J., Davey, C.A. Description: Nucleosome core particle with an adduct of a b...

New page

'''Unreleased structure'''

The entry 5xf6 is ON HOLD

Authors: Ma, Z., Adhireksan, Z., Murray, B.S., Dyson, P.J., Davey, C.A.

Description: Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane) compound having an ethylenediamine linker
[[Category: Unreleased Structures]]
[[Category: Dyson, P.J]]
[[Category: Adhireksan, Z]]
[[Category: Davey, C.A]]
[[Category: Murray, B.S]]
[[Category: Ma, Z]]