2kde: Difference between revisions

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OCA

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 ==NMR structure of major S5a (196-306):K48 linked diubiquitin species==
-<StructureSection load='2kde' size='340' side='right'caption='[[2kde]], [[NMR_Ensembles_of_Models | 7 NMR models]]' scene=''>
+<StructureSection load='2kde' size='340' side='right'caption='[[2kde]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2kde]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/African_clawed_frog African clawed frog] and [https://en.wikipedia.org/wiki/Human Human]. 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>
+<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>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1yx4|1yx4]], [[1yx5|1yx5]], [[1yx6|1yx6]], [[1d3z|1d3z]], [[2kdf|2kdf]]</div></td></tr>
+</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PSMD4, MCB1 ([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=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>
 </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. [[https://www.uniprot.org/uniprot/UBIQP_XENLA UBIQP_XENLA]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling (By similarity).
+[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]]
@@ Line 15: / Line 14: @@
    <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/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 37: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: African clawed frog]]
+[[Category: Homo sapiens]]
-[[Category: Human]]
 [[Category: Large Structures]]
-[[Category: Cole, J L]]
+[[Category: Xenopus laevis]]
-[[Category: Ehlinger, A]]
+[[Category: Cole JL]]
-[[Category: Fushman, D]]
+[[Category: Ehlinger A]]
-[[Category: Haririnia, A]]
+[[Category: Fushman D]]
-[[Category: Kang, Y]]
+[[Category: Haririnia A]]
-[[Category: Lary, J W]]
+[[Category: Kang Y]]
-[[Category: Randles, L]]
+[[Category: Lary JW]]
-[[Category: Walters, K J]]
+[[Category: Randles L]]
-[[Category: Wang, Q]]
+[[Category: Walters KJ]]
-[[Category: Zhang, N]]
+[[Category: Wang Q]]
-[[Category: Alternative splicing]]
+[[Category: Zhang N]]
-[[Category: Cytoplasm]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Proteasome]]
-[[Category: Protein binding]]
-[[Category: Protein complex]]
-[[Category: Ubiquitin interacting motif]]
-[[Category: Ubl conjugation]]