2kde: Difference between revisions

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-[[Image:2kde.png|left|200px]]
-<!--
+==NMR structure of major S5a (196-306):K48 linked diubiquitin species==
-The line below this paragraph, containing "STRUCTURE_2kde", creates the "Structure Box" on the page.
+<StructureSection load='2kde' size='340' side='right'caption='[[2kde]]' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2kde]] is a 3 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 experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KDE FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 7 models</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=2kde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kde OCA], [https://pdbe.org/2kde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kde RCSB], [https://www.ebi.ac.uk/pdbsum/2kde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kde ProSAT]</span></td></tr>
-{{STRUCTURE_2kde|  PDB=2kde  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PSMD4_HUMAN PSMD4_HUMAN] Binds and presumably selects ubiquitin-conjugates for destruction. Displays selectivity for longer polyubiquitin chains. Modulates intestinal fluid secretion.
+== 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/kd/2kde_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2kde ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Degradation by the proteasome typically requires substrate ubiquitination. Two ubiquitin receptors exist in the proteasome, S5a/Rpn10 and Rpn13. Whereas Rpn13 has only one ubiquitin-binding surface, S5a binds ubiquitin with two independent ubiquitin-interacting motifs (UIMs). Here, we use nuclear magnetic resonance (NMR) and analytical ultracentrifugation to define at atomic level resolution how S5a binds K48-linked diubiquitin, in which K48 of one ubiquitin subunit (the "proximal" one) is covalently bonded to G76 of the other (the "distal" subunit). We demonstrate that S5a's UIMs bind the two subunits simultaneously with a preference for UIM2 binding to the proximal subunit while UIM1 binds to the distal one. In addition, NMR experiments reveal that Rpn13 and S5a bind K48-linked diubiquitin simultaneously with subunit specificity, and a model structure of S5a and Rpn13 bound to K48-linked polyubiquitin is provided. Altogether, our data demonstrate that S5a is highly adaptive and cooperative toward binding ubiquitin chains.
-===NMR structure of major S5a (196-306):K48 linked diubiquitin species===
+Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13.,Zhang N, Wang Q, Ehlinger A, Randles L, Lary JW, Kang Y, Haririnia A, Storaska AJ, Cole JL, Fushman D, Walters KJ Mol Cell. 2009 Aug 14;35(3):280-90. PMID:19683493<ref>PMID:19683493</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_19683493}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2kde" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 19683493 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_19683493}}
-==About this Structure==
-[[2kde]] is a 3 chain structure of [[Ubiquitin]] with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KDE OCA].
 ==See Also==
-*[[Ubiquitin]]
+*[[Proteasome 3D structures|Proteasome 3D structures]]
+*[[3D structures of ubiquitin|3D structures of ubiquitin]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:19683493</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
+[[Category: Large Structures]]
 [[Category: Xenopus laevis]]
-[[Category: Cole, J L.]]
+[[Category: Cole JL]]
-[[Category: Ehlinger, A.]]
+[[Category: Ehlinger A]]
-[[Category: Fushman, D.]]
+[[Category: Fushman D]]
-[[Category: Haririnia, A.]]
+[[Category: Haririnia A]]
-[[Category: Kang, Y.]]
+[[Category: Kang Y]]
-[[Category: Lary, J W.]]
+[[Category: Lary JW]]
-[[Category: Randles, L.]]
+[[Category: Randles L]]
-[[Category: Walters, K J.]]
+[[Category: Walters KJ]]
-[[Category: Wang, Q.]]
+[[Category: Wang Q]]
-[[Category: Zhang, N.]]
+[[Category: Zhang N]]
-[[Category: Alternative splicing]]
-[[Category: Cytoplasm]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Proteasome]]
-[[Category: Protein binding]]
-[[Category: Protein complex]]
-[[Category: Ubiquitin interacting motif]]
-[[Category: Ubl conjugation]]