1ur6: Difference between revisions

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-[[Image:1ur6.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1ur6", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1ur6|  PDB=1ur6  |  SCENE=  }}
-'''NMR BASED STRUCTURAL MODEL OF THE UBCH5B-CNOT4 COMPLEX'''
+==NMR based structural model of the UbcH5B-CNOT4 complex==
+<StructureSection load='1ur6' size='340' side='right'caption='[[1ur6]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ur6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UR6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UR6 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Solution NMR , Theoretical Model</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1ur6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ur6 OCA], [https://pdbe.org/1ur6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ur6 RCSB], [https://www.ebi.ac.uk/pdbsum/1ur6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ur6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/UB2D2_HUMAN UB2D2_HUMAN] Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro catalyzes 'Lys-48'-linked polyubiquitination. Mediates the selective degradation of short-lived and abnormal proteins. Functions in the E6/E6-AP-induced ubiquitination of p53/TP53. Mediates ubiquitination of PEX5 and autoubiquitination of STUB1 and TRAF6. Involved in the signal-induced conjugation and subsequent degradation of NFKBIA, FBXW2-mediated GCM1 ubiquitination and degradation, MDM2-dependent degradation of p53/TP53 and the activation of MAVS in the mitochondria by DDX58/RIG-I in response to viral infection. Essential for viral activation of IRF3.<ref>PMID:10329681</ref> <ref>PMID:15280377</ref> <ref>PMID:18042044</ref> <ref>PMID:18703417</ref> <ref>PMID:18359941</ref> <ref>PMID:19854139</ref> <ref>PMID:20403326</ref> <ref>PMID:20061386</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/ur/1ur6_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/main_output.php?pdb_ID=1ur6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The protein CNOT4 possesses an N-terminal RING finger domain that acts as an E3 ubiquitin ligase and specifically interacts with UbcH5B, a ubiquitin-conjugating enzyme. The structure of the CNOT4 RING domain has been solved and the amino acids important for the binding to UbcH5B have been mapped. Here, the residues of UbcH5B important for the binding to CNOT4 RING domain were identified by NMR chemical shift perturbation experiments, and these data were used to generate structural models of the complex with the program HADDOCK. Together with the NMR data, additional biochemical data were included in a second docking, and comparisons of the resulting model with the structure of the c-Cbl/UbcH7 complex reveal some significant differences, notably at specific residues, and give structural insights into the E2/E3 specificity.
-==Overview==
+Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches.,Dominguez C, Bonvin AM, Winkler GS, van Schaik FM, Timmers HT, Boelens R Structure. 2004 Apr;12(4):633-44. PMID:15062086<ref>PMID:15062086</ref>
-The protein CNOT4 possesses an N-terminal RING finger domain that acts as an E3 ubiquitin ligase and specifically interacts with UbcH5B, a ubiquitin-conjugating enzyme. The structure of the CNOT4 RING domain has been solved and the amino acids important for the binding to UbcH5B have been mapped. Here, the residues of UbcH5B important for the binding to CNOT4 RING domain were identified by NMR chemical shift perturbation experiments, and these data were used to generate structural models of the complex with the program HADDOCK. Together with the NMR data, additional biochemical data were included in a second docking, and comparisons of the resulting model with the structure of the c-Cbl/UbcH7 complex reveal some significant differences, notably at specific residues, and give structural insights into the E2/E3 specificity.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-UR6 is a [[Protein complex]] structure of 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=1UR6 OCA].
+</div>
+<div class="pdbe-citations 1ur6" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches., Dominguez C, Bonvin AM, Winkler GS, van Schaik FM, Timmers HT, Boelens R, Structure. 2004 Apr;12(4):633-44. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15062086 15062086]
+*[[3D structures of ubiquitin conjugating enzyme|3D structures of ubiquitin conjugating enzyme]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Ubiquitin--protein ligase]]
+[[Category: Boelens R]]
-[[Category: Boelens, R.]]
+[[Category: Bonvin AMJJ]]
-[[Category: Bonvin, A M.J J.]]
+[[Category: Dominguez C]]
-[[Category: Dominguez, C.]]
+[[Category: Timmers HThM]]
-[[Category: Schaik, F M.A Van.]]
+[[Category: Van Schaik FMA]]
-[[Category: Timmers, H Th M.]]
+[[Category: Winkler GS]]
-[[Category: Winkler, G S.]]
-[[Category: Ccr4-not complex]]
-[[Category: Ligase]]
-[[Category: Ring finger protein]]
-[[Category: Transcription regulation]]
-[[Category: Ubiquitin conjugating enzyme]]
-[[Category: Ubiquitin ligase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 11:34:37 2008''