1oby: Difference between revisions

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-[[Image:1oby.gif|left|200px]]
- {{Structure
+==Crystal structure of the complex of PDZ2 of syntenin with a syndecan-4 peptide.==
-|PDB= 1oby |SIZE=350|CAPTION= <scene name='initialview01'>1oby</scene>, resolution 1.85&Aring;
+<StructureSection load='1oby' size='340' side='right'caption='[[1oby]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:So4+Binding+Site+For+Chain+A'>AC1</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+<table><tr><td colspan='2'>[[1oby]] is a 4 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=1OBY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OBY FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
-|GENE=
+<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>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1oby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oby OCA], [https://pdbe.org/1oby PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oby RCSB], [https://www.ebi.ac.uk/pdbsum/1oby PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oby ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1oby FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oby OCA], [http://www.ebi.ac.uk/pdbsum/1oby PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1oby RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/SDCB1_HUMAN SDCB1_HUMAN] Seems to function as an adapter protein. In adherens junctions may function to couple syndecans to cytoskeletal proteins or signaling components. Seems to couple transcription factor SOX4 to the IL-5 receptor (IL5RA). May also play a role in vesicular trafficking. Seems to be required for the targeting of TGFA to the cell surface in the early secretory pathway.<ref>PMID:10230395</ref> <ref>PMID:11179419</ref> <ref>PMID:11498591</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/ob/1oby_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=1oby ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Crystal structures of the PDZ2 domain of the scaffolding protein syntenin, both unbound and in complexes with peptides derived from C termini of IL5 receptor (alpha chain) and syndecan, reveal the molecular roots of syntenin's degenerate specificity. Three distinct binding sites (S(0), S(-1), and S(-2)), with affinities for hydrophobic side chains, function in a combinatorial way: S(-1) and S(-2) act together to bind syndecan, while S(0) and S(-1) are involved in the binding of IL5Ralpha. Neither mode of interaction is consistent with the prior classification scheme, which defined the IL5Ralpha interaction as class I (-S/T-X-phi) and the syndecan interaction as class II (-phi-X-phi). These results, in conjunction with other emerging structural data on PDZ domains, call for a revision of their classification and of the existing model of their mechanism.
-'''CRYSTAL STRUCTURE OF THE COMPLEX OF PDZ2 OF SYNTENIN WITH A SYNDECAN-4 PEPTIDE.'''
+Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm.,Kang BS, Cooper DR, Devedjiev Y, Derewenda U, Derewenda ZS Structure. 2003 Jul;11(7):845-53. PMID:12842047<ref>PMID:12842047</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1oby" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Crystal structures of the PDZ2 domain of the scaffolding protein syntenin, both unbound and in complexes with peptides derived from C termini of IL5 receptor (alpha chain) and syndecan, reveal the molecular roots of syntenin's degenerate specificity. Three distinct binding sites (S(0), S(-1), and S(-2)), with affinities for hydrophobic side chains, function in a combinatorial way: S(-1) and S(-2) act together to bind syndecan, while S(0) and S(-1) are involved in the binding of IL5Ralpha. Neither mode of interaction is consistent with the prior classification scheme, which defined the IL5Ralpha interaction as class I (-S/T-X-phi) and the syndecan interaction as class II (-phi-X-phi). These results, in conjunction with other emerging structural data on PDZ domains, call for a revision of their classification and of the existing model of their mechanism.
+*[[3D structures of syntenin|3D structures of syntenin]]
+== References ==
-==About this Structure==
+<references/>
-OBY 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=1OBY OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm., Kang BS, Cooper DR, Devedjiev Y, Derewenda U, Derewenda ZS, Structure. 2003 Jul;11(7):845-53. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12842047 12842047]
 [[Category: Homo sapiens]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Cooper, D R.]]
+[[Category: Cooper DR]]
-[[Category: Derewenda, U.]]
+[[Category: Derewenda U]]
-[[Category: Derewenda, Z S.]]
+[[Category: Derewenda ZS]]
-[[Category: Devedjiev, Y.]]
+[[Category: Devedjiev Y]]
-[[Category: Kang, B S.]]
+[[Category: Kang BS]]
-[[Category: pdz domain]]
-[[Category: signal transduction,nuclear protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:43:01 2008''