3h8h: Difference between revisions

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 ==Structure of the C-terminal domain of human RNF2/RING1B;==
-<StructureSection load='3h8h' size='340' side='right' caption='[[3h8h]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='3h8h' size='340' side='right'caption='[[3h8h]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3h8h]] is a 1 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=3H8H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3H8H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3h8h]] is a 1 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=3H8H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3H8H FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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&#8491;</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])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2PE:NONAETHYLENE+GLYCOL'>2PE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3h8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h8h OCA], [http://pdbe.org/3h8h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3h8h RCSB], [http://www.ebi.ac.uk/pdbsum/3h8h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3h8h 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=3h8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3h8h OCA], [https://pdbe.org/3h8h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3h8h RCSB], [https://www.ebi.ac.uk/pdbsum/3h8h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3h8h ProSAT]</span></td></tr>
 </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>
+[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 ==
 [[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/h8/3h8h_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h8/3h8h_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 20: / 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=3h8h ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Polycomb group (PcG) proteins are a special set of repressive transcription factors involved in epigenetic modifications of chromatin. They form two functionally distinct groups of catalytically active complexes: Polycomb repressive complex 1 (PRC1) and 2 (PRC2). The PRC1 complex is an important yet poorly characterized multiprotein histone ubiquitylation machine responsible for maintaining transcriptionally silent states of genes through histone H2A K119 modification. The Ring domain containing subunits of PRC1 also have substrate-targeting domains that interact with Cbx proteins, which have been implicated in chromatin and RNA binding. In this work, we present a high resolution structure of the C-terminal domain of Ring1B, revealing a variant ubiquitin-like fold with a distinct conserved surface region. On the basis of crystal structure and mutational analysis of this domain we show that the conserved surface is responsible for interaction with Cbx members of the PRC1 and homodimer formation. These data suggest a mechanism by which Ring1B serves as an adaptor that mediates binding between the members of the PRC1 complex and the nucleosome.
-Ring1B contains a ubiquitin-like docking module for interaction with Cbx proteins.,Bezsonova I, Walker JR, Bacik JP, Duan S, Dhe-Paganon S, Arrowsmith CH Biochemistry. 2009 Nov 10;48(44):10542-8. PMID:19791798<ref>PMID:19791798</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3h8h" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Ubiquitin protein ligase|Ubiquitin protein ligase]]
+*[[Ubiquitin protein ligase 3D structures|Ubiquitin protein ligase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Arrowsmith, C H]]
+[[Category: Large Structures]]
-[[Category: Bacik, J]]
+[[Category: Arrowsmith CH]]
-[[Category: Bezsonova, I]]
+[[Category: Bacik J]]
-[[Category: Bochkarev, A]]
+[[Category: Bezsonova I]]
-[[Category: Bountra, C]]
+[[Category: Bochkarev A]]
-[[Category: Dhe-Paganon, S]]
+[[Category: Bountra C]]
-[[Category: Duan, S]]
+[[Category: Dhe-Paganon S]]
-[[Category: Edwards, A M]]
+[[Category: Duan S]]
-[[Category: Structural genomic]]
+[[Category: Edwards AM]]
-[[Category: Walker, J R]]
+[[Category: Walker JR]]
-[[Category: Weigelt, J]]
+[[Category: Weigelt J]]
-[[Category: Chromatin regulator]]
-[[Category: Chromosomal protein]]
-[[Category: E3-ligase]]
-[[Category: Ligase]]
-[[Category: Metal-binding]]
-[[Category: Nuclear protein]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Polycomb]]
-[[Category: Proto-oncogene]]
-[[Category: Repressor]]
-[[Category: Ring1b]]
-[[Category: Sgc]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transcription regulation complex]]
-[[Category: Ubiquitin fold]]
-[[Category: Ubl conjugation pathway]]
-[[Category: Zinc-finger]]