6iq4 - Revision history

OCA at 10:34, 27 March 2024

OCA — Wed, 27 Mar 2024 10:34:48 GMT

←Older revision		Revision as of 10:34, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6iq4' size='340' side='right'caption='[[6iq4]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6iq4' size='340' side='right'caption='[[6iq4]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6iq4]] 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=6IQ4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IQ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6iq4]] 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=6IQ4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IQ4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=D0X:[Ru(eta(6)-p-cymene)Cl-2(pta)'>D0X</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XIS:4-diphenylphosphanylbenzoic+acid'>XIS</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]] 2.25Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J ([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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=D0X:[Ru(eta(6)-p-cymene)Cl-2(pta)'>D0X</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XIS:4-diphenylphosphanylbenzoic+acid'>XIS</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=6iq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iq4 OCA], [~~http~~://pdbe.org/6iq4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6iq4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6iq4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6iq4 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=6iq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iq4 OCA], [https://pdbe.org/6iq4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6iq4 RCSB], [https://www.ebi.ac.uk/pdbsum/6iq4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6iq4 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;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Targeting defined histone protein sites in chromatin is an emerging therapeutic approach that can potentially be enhanced by allosteric effects within the nucleosome. Here we characterized a novel hetero-bimetallic compound with a design based on a nucleosomal allostery effect observed earlier for two unrelated drugs-the Ru(II) antimetastasis/antitumor RAPTA-T and the Au(I) anti-arthritic auranofin. The Ru(II) moiety binds specifically to two H2A glutamate residues on the nucleosome acidic patch, allosterically triggering a cascade of structural changes that promote binding of the Au(I) moiety to selective histidine residues on H3, resulting in cross-linking sites that are over 35 A distant. By tethering the H2A-H2B dimers to the H3-H4 tetramer, the hetero-bimetallic compound significantly increases stability of the nucleosome, illustrating its utility as a site-selective cross-linking agent.	+

-	Crosslinking Allosteric Sites on the Nucleosome.,Batchelor LK, De Falco L, von Erlach T, Sharma D, Adhireksan Z, Roethlisberger U, Davey CA, Dyson PJ Angew Chem Int Ed Engl. 2019 Oct 28;58(44):15660-15664. doi:, 10.1002/anie.201906423. Epub 2019 Sep 18. PMID:31478581<ref>PMID:31478581</ref>	+	==See Also==
-		+	*[[Histone 3D structures\|Histone 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6iq4" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Adhireksan, Z]]	+	[[Category: Adhireksan Z]]
-	[[Category: Batchelor~~, L K~~]]	+	[[Category: Batchelor LK]]
-	[[Category: Davey~~, C A~~]]	+	[[Category: Davey CA]]
-	[[Category: DeFalco, L]]	+	[[Category: DeFalco L]]
-	[[Category: Dyson~~, P J]]~~	+	[[Category: Dyson PJ]]
-	~~[[Category: Anticancer]]~~	+
-	~~[[Category: Cross-link]]~~	+
-	~~[[Category: Dna binding protein-dna complex]]~~	+
-	~~[[Category: Gold]]~~	+
-	~~[[Category: Nucleosome]]~~	+
-	~~[[Category: Organometallic]]~~	+
-	~~[[Category: Ruthenium~~]]	+

OCA at 07:59, 6 November 2019

OCA — Wed, 06 Nov 2019 07:59:27 GMT

←Older revision		Revision as of 07:59, 6 November 2019
Line 3:		Line 3:
	<StructureSection load='6iq4' size='340' side='right'caption='[[6iq4]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6iq4' size='340' side='right'caption='[[6iq4]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6iq4]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IQ4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6iq4]] 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=6IQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IQ4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=D0X:[Ru(eta(6)-p-cymene)Cl-2(pta)'>D0X</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XIS:4-diphenylphosphanylbenzoic+acid'>XIS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=D0X:[Ru(eta(6)-p-cymene)Cl-2(pta)'>D0X</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XIS:4-diphenylphosphanylbenzoic+acid'>XIS</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J ([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=6iq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iq4 OCA], [http://pdbe.org/6iq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iq4 RCSB], [http://www.ebi.ac.uk/pdbsum/6iq4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iq4 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=6iq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iq4 OCA], [http://pdbe.org/6iq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iq4 RCSB], [http://www.ebi.ac.uk/pdbsum/6iq4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iq4 ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Adhireksan, Z]]		[[Category: Adhireksan, Z]]

OCA at 09:00, 30 October 2019

OCA — Wed, 30 Oct 2019 09:00:39 GMT

←Older revision		Revision as of 09:00, 30 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6iq4 is ~~ON HOLD~~	+	==Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups.==
		+	<StructureSection load='6iq4' size='340' side='right'caption='[[6iq4]], [[Resolution\|resolution]] 2.25Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6iq4]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IQ4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IQ4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=D0X:[Ru(eta(6)-p-cymene)Cl-2(pta)'>D0X</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XIS:4-diphenylphosphanylbenzoic+acid'>XIS</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=6iq4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6iq4 OCA], [http://pdbe.org/6iq4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6iq4 RCSB], [http://www.ebi.ac.uk/pdbsum/6iq4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6iq4 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 ==
		+	Targeting defined histone protein sites in chromatin is an emerging therapeutic approach that can potentially be enhanced by allosteric effects within the nucleosome. Here we characterized a novel hetero-bimetallic compound with a design based on a nucleosomal allostery effect observed earlier for two unrelated drugs-the Ru(II) antimetastasis/antitumor RAPTA-T and the Au(I) anti-arthritic auranofin. The Ru(II) moiety binds specifically to two H2A glutamate residues on the nucleosome acidic patch, allosterically triggering a cascade of structural changes that promote binding of the Au(I) moiety to selective histidine residues on H3, resulting in cross-linking sites that are over 35 A distant. By tethering the H2A-H2B dimers to the H3-H4 tetramer, the hetero-bimetallic compound significantly increases stability of the nucleosome, illustrating its utility as a site-selective cross-linking agent.

-	~~Authors: DeFalco, L~~., Batchelor, L~~.K.~~, ~~Adhireksan~~, Z., ~~Dyson~~, P.J., ~~Davey, C~~.A.	+	Crosslinking Allosteric Sites on the Nucleosome.,Batchelor LK, De Falco L, von Erlach T, Sharma D, Adhireksan Z, Roethlisberger U, Davey CA, Dyson PJ Angew Chem Int Ed Engl. 2019 Oct 28;58(44):15660-15664. doi:, 10.1002/anie.201906423. Epub 2019 Sep 18. PMID:31478581<ref>PMID:31478581</ref>

-	~~Description: Nucleosome core particle cross-linked with~~ a ~~hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Dyson, P.J~~]]	+	<div class="pdbe-citations 6iq4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Adhireksan, Z]]		[[Category: Adhireksan, Z]]
-	[[Category: Davey, C.A]]	+	[[Category: Batchelor, L K]]
-	[[Category: ~~Batchelor~~, L.K]]	+	[[Category: Davey, C A]]
-	[[Category: ~~Defalco~~, L]]	+	[[Category: DeFalco, L]]
		+	[[Category: Dyson, P J]]
		+	[[Category: Anticancer]]
		+	[[Category: Cross-link]]
		+	[[Category: Dna binding protein-dna complex]]
		+	[[Category: Gold]]
		+	[[Category: Nucleosome]]
		+	[[Category: Organometallic]]
		+	[[Category: Ruthenium]]

OCA: Protected "6iq4" [edit=sysop:move=sysop]

OCA — Wed, 14 Nov 2018 06:32:36 GMT

Protected "6iq4" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:32, 14 November 2018

OCA: New page: '''Unreleased structure''' The entry 6iq4 is ON HOLD Authors: DeFalco, L., Batchelor, L.K., Adhireksan, Z., Dyson, P.J., Davey, C.A. Description: Nucleosome core particle cross-linked ...

OCA — Wed, 14 Nov 2018 06:32:34 GMT

New page: '''Unreleased structure''' The entry 6iq4 is ON HOLD Authors: DeFalco, L., Batchelor, L.K., Adhireksan, Z., Dyson, P.J., Davey, C.A. Description: Nucleosome core particle cross-linked ...

New page

'''Unreleased structure'''

The entry 6iq4 is ON HOLD

Authors: DeFalco, L., Batchelor, L.K., Adhireksan, Z., Dyson, P.J., Davey, C.A.

Description: Nucleosome core particle cross-linked with a hetero-binuclear molecule possessing RAPTA and gold(I) 4-(diphenylphosphino)benzoic acid groups.
[[Category: Unreleased Structures]]
[[Category: Dyson, P.J]]
[[Category: Adhireksan, Z]]
[[Category: Davey, C.A]]
[[Category: Batchelor, L.K]]
[[Category: Defalco, L]]