3ixs - Revision history

OCA at 10:07, 21 February 2024

OCA — Wed, 21 Feb 2024 10:07:26 GMT

←Older revision		Revision as of 10:07, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3ixs' size='340' side='right'caption='[[3ixs]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='3ixs' size='340' side='right'caption='[[3ixs]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ixs]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ixs]] is a 12 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=3IXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IXS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=NHE:2-~~[~~N-CYCLOHEXYLAMINO~~]~~ETHANE+SULFONIC+ACID'>NHE</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]] 1.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[3gs2\|3gs2]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>~~[~~[Gene\|Gene:~~]~~]</b~~></td><td class="sblockDat">BAP1, DING, HIPI3, RING1B, RNF2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), DEDAF, RYBP, YEAF1 ([https://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=3ixs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ixs OCA], [https://pdbe.org/3ixs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ixs RCSB], [https://www.ebi.ac.uk/pdbsum/3ixs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ixs 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=3ixs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ixs OCA], [https://pdbe.org/3ixs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ixs RCSB], [https://www.ebi.ac.uk/pdbsum/3ixs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ixs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RING2_HUMAN RING2_HUMAN]] E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. E3 ubiquitin-protein ligase activity is enhanced by BMI1/PCGF4. Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity.<ref>PMID:11513855</ref> <ref>PMID:15386022</ref> <ref>PMID:16359901</ref> <ref>PMID:16714294</ref> <ref>PMID:20696397</ref> [[https://www.uniprot.org/uniprot/RYBP_HUMAN RYBP_HUMAN]] Inhibits ubiquitination and subsequent degradation of TP53, and thereby plays a role in regulating transcription of TP53 target genes. May be implicated in the regulation of the transcription as a repressor of the transcriptional activity of E4TF1. May bind to DNA. Promotes apoptosis.<ref>PMID:11395500</ref> <ref>PMID:11953439</ref> <ref>PMID:14765135</ref> <ref>PMID:19098711</ref>	+	[https://www.uniprot.org/uniprot/RING2_HUMAN RING2_HUMAN] E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. E3 ubiquitin-protein ligase activity is enhanced by BMI1/PCGF4. Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity.<ref>PMID:11513855</ref> <ref>PMID:15386022</ref> <ref>PMID:16359901</ref> <ref>PMID:16714294</ref> <ref>PMID:20696397</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ixs ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ixs ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	RING1B, a Polycomb Group (PcG) protein, binds methylated chromatin through its association with another PcG protein called Polycomb (Pc). However, RING1B can associate with nonmethylated chromatin suggesting an alternate mechanism for RING1B interaction with chromatin. Here, we demonstrate that two proteins with little sequence identity between them, the Pc cbox domain and RYBP, bind the same surface on the C-terminal domain of RING1B (C-RING1B). Pc cbox and RYBP each fold into a nearly identical, intermolecular beta sheet with C-RING1B and a loop structure which are completely different in the two proteins. Both the beta sheet and loop are required for stable binding and transcription repression. Further, a mutation engineered to disrupt binding on the Drosophila dRING1 protein prevents chromatin association and PcG function in vivo. These results suggest that PcG targeting to different chromatin locations relies, in part, on binding partners of C-RING1B that are diverse in sequence and structure.
-
-	Polycomb group targeting through different binding partners of RING1B C-terminal domain.,Wang R, Taylor AB, Leal BZ, Chadwell LV, Ilangovan U, Robinson AK, Schirf V, Hart PJ, Lafer EM, Demeler B, Hinck AP, McEwen DG, Kim CA Structure. 2010 Aug 11;18(8):966-75. PMID:20696397<ref>PMID:20696397</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3ixs" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim~~, C A~~]]	+	[[Category: Kim CA]]
-	[[Category: Taylor~~, A B~~]]	+	[[Category: Taylor AB]]
-	[[Category: Wang, R]]	+	[[Category: Wang R]]
-	~~[[Category: Apoptosis]]~~	+
-	~~[[Category: Chromatin regulator]]~~	+
-	~~[[Category: Chromosomal protein]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: E3-ligase]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Polycomb]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Repressor]]~~	+
-	~~[[Category: Ring1b]]~~	+
-	~~[[Category: Rybp]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation]]~~	+
-	~~[[Category: Transcription repressor]]~~	+
-	~~[[Category: Ubl conjugation pathway]]~~	+
-	~~[[Category: Zinc-finger~~]]	+

OCA at 12:16, 13 October 2021

OCA — Wed, 13 Oct 2021 12:16:30 GMT

←Older revision		Revision as of 12:16, 13 October 2021
Line 1:		Line 1:

	==Ring1B C-terminal domain/RYBP C-terminal domain Complex==		==Ring1B C-terminal domain/RYBP C-terminal domain Complex==
-	<StructureSection load='3ixs' size='340' side='right' caption='[[3ixs]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='3ixs' size='340' side='right'caption='[[3ixs]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ixs]] is a 12 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=3IXS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ixs]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IXS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gs2\|3gs2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3gs2\|3gs2]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAP1, DING, HIPI3, RING1B, RNF2 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), DEDAF, RYBP, YEAF1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAP1, DING, HIPI3, RING1B, RNF2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), DEDAF, RYBP, YEAF1 ([https://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=3ixs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ixs OCA], [~~http~~://pdbe.org/3ixs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ixs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ixs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ixs 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=3ixs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ixs OCA], [https://pdbe.org/3ixs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ixs RCSB], [https://www.ebi.ac.uk/pdbsum/3ixs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ixs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RING2_HUMAN RING2_HUMAN]] E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. E3 ubiquitin-protein ligase activity is enhanced by BMI1/PCGF4. Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity.<ref>PMID:11513855</ref> <ref>PMID:15386022</ref> <ref>PMID:16359901</ref> <ref>PMID:16714294</ref> <ref>PMID:20696397</ref> [[~~http~~://www.uniprot.org/uniprot/RYBP_HUMAN RYBP_HUMAN]] Inhibits ubiquitination and subsequent degradation of TP53, and thereby plays a role in regulating transcription of TP53 target genes. May be implicated in the regulation of the transcription as a repressor of the transcriptional activity of E4TF1. May bind to DNA. Promotes apoptosis.<ref>PMID:11395500</ref> <ref>PMID:11953439</ref> <ref>PMID:14765135</ref> <ref>PMID:19098711</ref>	+	[[https://www.uniprot.org/uniprot/RING2_HUMAN RING2_HUMAN]] E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. E3 ubiquitin-protein ligase activity is enhanced by BMI1/PCGF4. Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity.<ref>PMID:11513855</ref> <ref>PMID:15386022</ref> <ref>PMID:16359901</ref> <ref>PMID:16714294</ref> <ref>PMID:20696397</ref> [[https://www.uniprot.org/uniprot/RYBP_HUMAN RYBP_HUMAN]] Inhibits ubiquitination and subsequent degradation of TP53, and thereby plays a role in regulating transcription of TP53 target genes. May be implicated in the regulation of the transcription as a repressor of the transcriptional activity of E4TF1. May bind to DNA. Promotes apoptosis.<ref>PMID:11395500</ref> <ref>PMID:11953439</ref> <ref>PMID:14765135</ref> <ref>PMID:19098711</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[Ubiquitin protein ligase\|Ubiquitin protein ligase]]	+	*[[Ubiquitin protein ligase 3D structures\|Ubiquitin protein ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Kim, C A]]		[[Category: Kim, C A]]
	[[Category: Taylor, A B]]		[[Category: Taylor, A B]]

OCA at 10:05, 19 December 2018

OCA — Wed, 19 Dec 2018 10:05:42 GMT

←Older revision		Revision as of 10:05, 19 December 2018
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ix/3ixs_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ix/3ixs_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 15:24, 4 August 2016

OCA — Thu, 04 Aug 2016 15:24:11 GMT

←Older revision		Revision as of 15:24, 4 August 2016
Line 1:		Line 1:
		+
	==Ring1B C-terminal domain/RYBP C-terminal domain Complex==		==Ring1B C-terminal domain/RYBP C-terminal domain Complex==
	<StructureSection load='3ixs' size='340' side='right' caption='[[3ixs]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='3ixs' size='340' side='right' caption='[[3ixs]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ixs]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ixs]] is a 12 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=3IXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IXS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gs2\|3gs2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gs2\|3gs2]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAP1, DING, HIPI3, RING1B, RNF2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~]), DEDAF, RYBP, YEAF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAP1, DING, HIPI3, RING1B, RNF2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), DEDAF, RYBP, YEAF1 ([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=3ixs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ixs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ixs RCSB], [http://www.ebi.ac.uk/pdbsum/3ixs PDBsum]</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=3ixs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ixs OCA], [http://pdbe.org/3ixs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ixs RCSB], [http://www.ebi.ac.uk/pdbsum/3ixs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ixs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ixs ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3ixs" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Kim, C A]]		[[Category: Kim, C A]]
	[[Category: Taylor, A B]]		[[Category: Taylor, A B]]

OCA at 10:31, 25 December 2014

OCA — Thu, 25 Dec 2014 10:31:58 GMT

←Older revision		Revision as of 10:31, 25 December 2014
Line 8:		Line 8:
	<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=3ixs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ixs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ixs RCSB], [http://www.ebi.ac.uk/pdbsum/3ixs PDBsum]</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=3ixs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ixs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ixs RCSB], [http://www.ebi.ac.uk/pdbsum/3ixs PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RING2_HUMAN RING2_HUMAN]] E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. E3 ubiquitin-protein ligase activity is enhanced by BMI1/PCGF4. Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity.<ref>PMID:11513855</ref> <ref>PMID:15386022</ref> <ref>PMID:16359901</ref> <ref>PMID:16714294</ref> <ref>PMID:20696397</ref> [[http://www.uniprot.org/uniprot/RYBP_HUMAN RYBP_HUMAN]] Inhibits ubiquitination and subsequent degradation of TP53, and thereby plays a role in regulating transcription of TP53 target genes. May be implicated in the regulation of the transcription as a repressor of the transcriptional activity of E4TF1. May bind to DNA. Promotes apoptosis.<ref>PMID:11395500</ref> <ref>PMID:11953439</ref> <ref>PMID:14765135</ref> <ref>PMID:19098711</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 17:13, 18 December 2014

OCA — Thu, 18 Dec 2014 17:13:25 GMT

←Older revision		Revision as of 17:13, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3ixs\| PDB=3ixs \| SCENE= }}~~	+	==Ring1B C-terminal domain/RYBP C-terminal domain Complex==
-	===Ring1B C-terminal domain/RYBP C-terminal domain Complex===	+	<StructureSection load='3ixs' size='340' side='right' caption='[[3ixs]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20696397}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ixs]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IXS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NHE:2-[N-CYCLOHEXYLAMINO]ETHANE+SULFONIC+ACID'>NHE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3gs2\|3gs2]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BAP1, DING, HIPI3, RING1B, RNF2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), DEDAF, RYBP, YEAF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3ixs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ixs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ixs RCSB], [http://www.ebi.ac.uk/pdbsum/3ixs PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ix/3ixs_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RING1B, a Polycomb Group (PcG) protein, binds methylated chromatin through its association with another PcG protein called Polycomb (Pc). However, RING1B can associate with nonmethylated chromatin suggesting an alternate mechanism for RING1B interaction with chromatin. Here, we demonstrate that two proteins with little sequence identity between them, the Pc cbox domain and RYBP, bind the same surface on the C-terminal domain of RING1B (C-RING1B). Pc cbox and RYBP each fold into a nearly identical, intermolecular beta sheet with C-RING1B and a loop structure which are completely different in the two proteins. Both the beta sheet and loop are required for stable binding and transcription repression. Further, a mutation engineered to disrupt binding on the Drosophila dRING1 protein prevents chromatin association and PcG function in vivo. These results suggest that PcG targeting to different chromatin locations relies, in part, on binding partners of C-RING1B that are diverse in sequence and structure.

-	~~==Function==~~	+	Polycomb group targeting through different binding partners of RING1B C-terminal domain.,Wang R, Taylor AB, Leal BZ, Chadwell LV, Ilangovan U, Robinson AK, Schirf V, Hart PJ, Lafer EM, Demeler B, Hinck AP, McEwen DG, Kim CA Structure. 2010 Aug 11;18(8):966-75. PMID:20696397<ref>PMID:20696397</ref>
-	~~[[http://www.uniprot.org/uniprot/RING2_HUMAN RING2_HUMAN]] E3 ubiquitin-protein ligase that mediates monoubiquitination~~ of ~~'Lys~~-~~119' of histone H2A, thereby playing a central role in histone code and gene regulation~~. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, ~~a complex class required to maintain the transcriptionally repressive state of many genes~~, ~~including Hox genes~~, ~~throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones~~, ~~rendering chromatin heritably changed in its expressibility~~. ~~E3 ubiquitin~~-~~protein ligase activity is enhanced by BMI1/PCGF4~~. Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity.<ref>PMID:11513855</ref><ref>PMID:15386022</ref><ref>PMID:16359901</ref><ref>PMID:~~16714294</ref>~~<ref>PMID:20696397</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3ixs]] is~~ a ~~12 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3IXS OCA].~~	+	</div>

	==See Also==		==See Also==
	*[[Ubiquitin protein ligase\|Ubiquitin protein ligase]]		*[[Ubiquitin protein ligase\|Ubiquitin protein ligase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:020696397</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Kim, C A.]]	+	[[Category: Kim, C A]]
-	[[Category: Taylor, A B.]]	+	[[Category: Taylor, A B]]
-	[[Category: Wang, R.]]	+	[[Category: Wang, R]]
	[[Category: Apoptosis]]		[[Category: Apoptosis]]
	[[Category: Chromatin regulator]]		[[Category: Chromatin regulator]]

OCA: Protected "3ixs" [edit=sysop:move=sysop]

OCA — Wed, 27 Mar 2013 09:34:41 GMT

Protected "3ixs" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:34, 27 March 2013

OCA at 09:34, 27 March 2013

OCA — Wed, 27 Mar 2013 09:34:30 GMT

←Older revision		Revision as of 09:34, 27 March 2013
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-	{{Seed}}
-	[[Image:3ixs.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ixs", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_3ixs\| PDB=3ixs \| SCENE= }}		{{STRUCTURE_3ixs\| PDB=3ixs \| SCENE= }}
-
	===Ring1B C-terminal domain/RYBP C-terminal domain Complex===		===Ring1B C-terminal domain/RYBP C-terminal domain Complex===
		+	{{ABSTRACT_PUBMED_20696397}}

		+	==Function==
		+	[[http://www.uniprot.org/uniprot/RING2_HUMAN RING2_HUMAN]] E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A, thereby playing a central role in histone code and gene regulation. H2A 'Lys-119' ubiquitination gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation. Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. E3 ubiquitin-protein ligase activity is enhanced by BMI1/PCGF4. Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity.<ref>PMID:11513855</ref><ref>PMID:15386022</ref><ref>PMID:16359901</ref><ref>PMID:16714294</ref><ref>PMID:20696397</ref>

-	~~<!--~~	+	==About this Structure==
-	~~The line below~~ this ~~paragraph, {{ABSTRACT_PUBMED_20696397}}, adds the Publication Abstract to the page~~	+	[[3ixs]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IXS OCA].
-	~~(as it appears on PubMed at~~ http://~~www~~.~~pubmed~~.~~gov), where 20696397~~ is ~~the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_20696397}}~~	+

-	==~~About this Structure~~==	+	==See Also==
-	~~3IXS is a 12 chains structure with sequences from~~ [~~http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens~~]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IXS OCA~~].	+	*[[Ubiquitin protein ligase\|Ubiquitin protein ligase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20696397~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020696397</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Kim, C A.]]		[[Category: Kim, C A.]]
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	[[Category: Ubl conjugation pathway]]		[[Category: Ubl conjugation pathway]]
	[[Category: Zinc-finger]]		[[Category: Zinc-finger]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 25 08:55:06 2010''

OCA at 04:47, 25 August 2010

OCA — Wed, 25 Aug 2010 04:47:16 GMT

←Older revision		Revision as of 04:47, 25 August 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3ixs.jpg\|left\|200px]]

-	The ~~entry 3ixs~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3ixs", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3ixs\| PDB=3ixs \| SCENE= }}

-	~~Authors: Wang, R., Taylor, A.B., Kim,~~ C~~.A.~~	+	===Ring1B C-terminal domain/RYBP C-terminal domain Complex===

-	Description: Ring1B C-terminal domain/RYBP C-terminal domain Complex

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Sep 30~~ 08:59:~~31 2009~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20696397}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20696397 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20696397}}
		+
		+	==About this Structure==
		+	3IXS is a 12 chains structure with sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IXS OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20696397</ref><references group="xtra"/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Kim, C A.]]
		+	[[Category: Taylor, A B.]]
		+	[[Category: Wang, R.]]
		+	[[Category: Apoptosis]]
		+	[[Category: Chromatin regulator]]
		+	[[Category: Chromosomal protein]]
		+	[[Category: Dna-binding]]
		+	[[Category: E3-ligase]]
		+	[[Category: Ligase]]
		+	[[Category: Metal-binding]]
		+	[[Category: Nucleus]]
		+	[[Category: Phosphoprotein]]
		+	[[Category: Polycomb]]
		+	[[Category: Protein binding]]
		+	[[Category: Repressor]]
		+	[[Category: Ring1b]]
		+	[[Category: Rybp]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]
		+	[[Category: Transcription repressor]]
		+	[[Category: Ubl conjugation pathway]]
		+	[[Category: Zinc-finger]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 25 08:55:06 2010''

OCA at 06:59, 30 September 2009

OCA — Wed, 30 Sep 2009 06:59:32 GMT

←Older revision		Revision as of 06:59, 30 September 2009
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3ixs is ON HOLD	+	The entry 3ixs is ON HOLD until Paper Publication

	Authors: Wang, R., Taylor, A.B., Kim, C.A.		Authors: Wang, R., Taylor, A.B., Kim, C.A.
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	Description: Ring1B C-terminal domain/RYBP C-terminal domain Complex		Description: Ring1B C-terminal domain/RYBP C-terminal domain Complex

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 16 08:45:04 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 30 08:59:31 2009''