1v1t

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[[Image:1v1t.gif|left|200px]]<br />
 
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<applet load="1v1t" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1v1t, resolution 1.80&Aring;" />
 
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'''CRYSTAL STRUCTURE OF THE PDZ TANDEM OF HUMAN SYNTENIN IN COMPLEX WITH TNEYKV PEPTIDE'''<br />
 
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==Overview==
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==Crystal structure of the PDZ tandem of human syntenin in complex with TNEYKV peptide==
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PDZ domains are among the most abundant protein modules in the known, genomes. Their main function is to provide scaffolds for, membrane-associated protein complexes by binding to the cytosolic, C-terminal fragments of receptors, channels, and other integral membrane, proteins. Here, using both heteronuclear NMR and single crystal X-ray, diffraction, we show how peptides with different sequences, including, those corresponding to the C-termini of syndecan, neurexin, and ephrin B, can simultaneously bind to both PDZ domains of the scaffolding protein, syntenin. The PDZ2 domain binds these peptides in the canonical fashion, and an induced fit mechanism allows for the accommodation of a range of, side chains in the P(0) and P(-)(2) positions. However, binding to the, PDZ1 domain requires that the target peptide assume a noncanonical, conformation. These data help explain how syntenin, and perhaps other, PDZ-containing proteins, may preferentially bind to dimeric and clustered, targets, and provide a mechanistic explanation for the previously reported, cooperative ligand binding by syntenin's two PDZ domains.
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<StructureSection load='1v1t' size='340' side='right'caption='[[1v1t]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1v1t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V1T FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BEZ:BENZOIC+ACID'>BEZ</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1v1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1t OCA], [https://pdbe.org/1v1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v1t RCSB], [https://www.ebi.ac.uk/pdbsum/1v1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v1t ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v1/1v1t_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1v1t ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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PDZ domains are among the most abundant protein modules in the known genomes. Their main function is to provide scaffolds for membrane-associated protein complexes by binding to the cytosolic, C-terminal fragments of receptors, channels, and other integral membrane proteins. Here, using both heteronuclear NMR and single crystal X-ray diffraction, we show how peptides with different sequences, including those corresponding to the C-termini of syndecan, neurexin, and ephrin B, can simultaneously bind to both PDZ domains of the scaffolding protein syntenin. The PDZ2 domain binds these peptides in the canonical fashion, and an induced fit mechanism allows for the accommodation of a range of side chains in the P(0) and P(-)(2) positions. However, binding to the PDZ1 domain requires that the target peptide assume a noncanonical conformation. These data help explain how syntenin, and perhaps other PDZ-containing proteins, may preferentially bind to dimeric and clustered targets, and provide a mechanistic explanation for the previously reported cooperative ligand binding by syntenin's two PDZ domains.
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==About this Structure==
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The binding of the PDZ tandem of syntenin to target proteins.,Grembecka J, Cierpicki T, Devedjiev Y, Derewenda U, Kang BS, Bushweller JH, Derewenda ZS Biochemistry. 2006 Mar 21;45(11):3674-83. PMID:16533050<ref>PMID:16533050</ref>
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1V1T is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with BEZ as [http://en.wikipedia.org/wiki/ligand ligand]. Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1V1T OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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The binding of the PDZ tandem of syntenin to target proteins., Grembecka J, Cierpicki T, Devedjiev Y, Derewenda U, Kang BS, Bushweller JH, Derewenda ZS, Biochemistry. 2006 Mar 21;45(11):3674-83. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16533050 16533050]
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</div>
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[[Category: Homo sapiens]]
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<div class="pdbe-citations 1v1t" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Cierpicki, T.]]
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[[Category: Cooper, D.]]
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[[Category: Derewenda, U.]]
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[[Category: Derewenda, Z.S.]]
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[[Category: Devedjiev, Y.]]
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[[Category: Grembecka, J.]]
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[[Category: BEZ]]
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[[Category: pdz domain]]
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[[Category: scaffolding protein]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 17:19:02 2007''
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==See Also==
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*[[3D structures of syntenin|3D structures of syntenin]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Synthetic construct]]
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[[Category: Cierpicki T]]
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[[Category: Cooper DR]]
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[[Category: Derewenda U]]
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[[Category: Derewenda ZS]]
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[[Category: Devedjiev Y]]
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[[Category: Grembecka J]]

Current revision

Crystal structure of the PDZ tandem of human syntenin in complex with TNEYKV peptide

PDB ID 1v1t

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