2efd: Difference between revisions

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 ==Ara7/AtVps9a==
-<StructureSection load='2efd' size='340' side='right' caption='[[2efd]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='2efd' size='340' side='right'caption='[[2efd]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2efd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EFD FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2efd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EFD FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2fec|2fec]], [[2efe|2efe]], [[2efh|2efh]]</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]] 3&#8491;</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=2efd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2efd RCSB], [http://www.ebi.ac.uk/pdbsum/2efd PDBsum]</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=2efd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efd OCA], [https://pdbe.org/2efd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2efd RCSB], [https://www.ebi.ac.uk/pdbsum/2efd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2efd ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Q9LT31_ARATH Q9LT31_ARATH]] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref>  [[http://www.uniprot.org/uniprot/Q9SN68_ARATH Q9SN68_ARATH]] Endosomal protein that may be involved in endocytosis.<ref>PMID:20833725</ref>
+[https://www.uniprot.org/uniprot/VPS9A_ARATH VPS9A_ARATH] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</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/ef/2efd_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ef/2efd_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].
+</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=2efd ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Many GTPases regulate intracellular transport and signaling in eukaryotes. Guanine nucleotide exchange factors (GEFs) activate GTPases by catalyzing the exchange of their GDP for GTP. Here we present crystallographic and biochemical studies of a GEF reaction with four crystal structures of Arabidopsis thaliana ARA7, a plant homolog of Rab5 GTPase, in complex with its GEF, VPS9a, in the nucleotide-free and GDP-bound forms, as well as a complex with aminophosphonic acid-guanylate ester and ARA7.VPS9a(D185N) with GDP. Upon complex formation with ARA7, VPS9 wedges into the interswitch region of ARA7, inhibiting the coordination of Mg(2+) and decreasing the stability of GDP binding. The aspartate finger of VPS9a recognizes GDP beta-phosphate directly and pulls the P-loop lysine of ARA7 away from GDP beta-phosphate toward switch II to further destabilize GDP for its release during the transition from the GDP-bound to nucleotide-free intermediates in the nucleotide exchange reaction.
-GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5.Vps9 system.,Uejima T, Ihara K, Goh T, Ito E, Sunada M, Ueda T, Nakano A, Wakatsuki S J Biol Chem. 2010 Nov 19;285(47):36689-97. Epub 2010 Sep 10. PMID:20833725<ref>PMID:20833725</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 == References ==
 <references/>
@@ Line 31: / Line 24: @@
 </StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Ihara, K]]
+[[Category: Large Structures]]
-[[Category: Uejima, T]]
+[[Category: Ihara K]]
-[[Category: Wakatsuki, S]]
+[[Category: Uejima T]]
-[[Category: Gef]]
+[[Category: Wakatsuki S]]
-[[Category: Gtpase]]
-[[Category: Nucleotide]]
-[[Category: Rab5]]
-[[Category: Transport protein]]
-[[Category: Vps9]]