2raj: Difference between revisions

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OCA

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 ==SO4 bound PX-BAR membrane remodeling unit of Sorting Nexin 9==
-<StructureSection load='2raj' size='340' side='right' caption='[[2raj]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
+<StructureSection load='2raj' size='340' side='right'caption='[[2raj]], [[Resolution|resolution]] 2.45&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2raj]] 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=2RAJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RAJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2raj]] 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=2RAJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RAJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 2.45&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2rai|2rai]], [[2rak|2rak]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SNX9, SH3PX1, SH3PXD3A ([http://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=2raj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2raj OCA], [https://pdbe.org/2raj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2raj RCSB], [https://www.ebi.ac.uk/pdbsum/2raj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2raj ProSAT]</span></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=2raj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2raj OCA], [http://pdbe.org/2raj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2raj RCSB], [http://www.ebi.ac.uk/pdbsum/2raj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2raj ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SNX9_HUMAN SNX9_HUMAN]] May be involved in several stages of intracellular trafficking. Plays a role in endocytosis via clathrin-coated pits, but also clathrin-independent, actin-dependent fluid-phase endocytosis. Plays a role in macropinocytosis. Promotes internalization of TNFR. Promotes degradation of EGFR after EGF signaling. Stimulates the GTPase activity of DNM1. Promotes DNM1 oligomerization. Promotes activation of the Arp2/3 complex by WASL, and thereby plays a role in the reorganization of the F-actin cytoskeleton. Binds to membranes enriched in phosphatidylinositol 4,5-bisphosphate and promotes membrane tubulation. Has lower affinity for membranes enriched in phosphatidylinositol 3-phosphate.<ref>PMID:11799118</ref> <ref>PMID:12952949</ref> <ref>PMID:15703209</ref> <ref>PMID:17609109</ref> <ref>PMID:18388313</ref> <ref>PMID:20427313</ref> <ref>PMID:21048941</ref> <ref>PMID:17948057</ref>
+[https://www.uniprot.org/uniprot/SNX9_HUMAN SNX9_HUMAN] May be involved in several stages of intracellular trafficking. Plays a role in endocytosis via clathrin-coated pits, but also clathrin-independent, actin-dependent fluid-phase endocytosis. Plays a role in macropinocytosis. Promotes internalization of TNFR. Promotes degradation of EGFR after EGF signaling. Stimulates the GTPase activity of DNM1. Promotes DNM1 oligomerization. Promotes activation of the Arp2/3 complex by WASL, and thereby plays a role in the reorganization of the F-actin cytoskeleton. Binds to membranes enriched in phosphatidylinositol 4,5-bisphosphate and promotes membrane tubulation. Has lower affinity for membranes enriched in phosphatidylinositol 3-phosphate.<ref>PMID:11799118</ref> <ref>PMID:12952949</ref> <ref>PMID:15703209</ref> <ref>PMID:17609109</ref> <ref>PMID:18388313</ref> <ref>PMID:20427313</ref> <ref>PMID:21048941</ref> <ref>PMID:17948057</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/ra/2raj_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ra/2raj_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 21: / 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=2raj ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Sorting nexins (SNXs) form a family of proteins known to interact with components in the endosomal system and to regulate various steps of vesicle transport. Sorting nexin 9 (SNX9) is involved in the late stages of clathrin-mediated endocytosis in non-neuronal cells, where together with the GTPase dynamin, it participates in the formation and scission of the vesicle neck. We report here crystal structures of the functional membrane-remodeling unit of SNX9 and show that it efficiently tubulates lipid membranes in vivo and in vitro. Elucidation of the protein superdomain structure, together with mutational analysis and biochemical and cell biological experiments, demonstrated how the SNX9 PX and BAR domains work in concert in targeting and tubulation of phosphoinositide-containing membranes. The study provides insights into the SNX9-induced membrane modulation mechanism.
-The PX-BAR membrane-remodeling unit of sorting nexin 9.,Pylypenko O, Lundmark R, Rasmuson E, Carlsson SR, Rak A EMBO J. 2007 Nov 14;26(22):4788-800. Epub 2007 Oct 18. PMID:17948057<ref>PMID:17948057</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2raj" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Sorting nexin|Sorting nexin]]
+*[[Sorting nexin 3D structures|Sorting nexin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Carlsson, S R]]
+[[Category: Large Structures]]
-[[Category: Lundmark, R]]
+[[Category: Carlsson SR]]
-[[Category: Pylypenko, O]]
+[[Category: Lundmark R]]
-[[Category: Rak, A]]
+[[Category: Pylypenko O]]
-[[Category: Rasmuson, E]]
+[[Category: Rak A]]
-[[Category: Bar domain]]
+[[Category: Rasmuson E]]
-[[Category: Membrane transport]]
-[[Category: Px domain]]
-[[Category: Sorting nexin]]
-[[Category: Structural protein]]
-[[Category: Tubulation]]