1r6j

From Proteopedia

(Difference between revisions)

Revision as of 07:12, 10 September 2015

Ultrahigh resolution Crystal Structure of syntenin PDZ2

Structural highlights

1r6j is a 1 chain structure with sequence from Human. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	SDCBP OR MDA9 OR SYCL (HUMAN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[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.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The crystal structure of the second PDZ domain of the scaffolding protein syntenin was solved using data extending to 0.73 A resolution. The crystallographic model, including the hydrogen atoms and the anisotropic displacement parameters, was refined to a conventional R-factor of 7.5% and Rfree of 8.7%, making it the most precise crystallographic model of a protein molecule to date. The model reveals discrete disorder in several places in the molecule, and significant plasticity of the peptide bond, with some omega angles deviating by nearly 20 degrees from planarity. Most hydrogen atoms are easily identifiable in the electron density and weak hydrogen bonds of the C-H...O type are clearly visible between the beta-strands. The study sets a new standard for high-resolution protein crystallography.

The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallography.,Kang BS, Devedjiev Y, Derewenda U, Derewenda ZS J Mol Biol. 2004 Apr 30;338(3):483-93. PMID:15081807^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Fernandez-Larrea J, Merlos-Suarez A, Urena JM, Baselga J, Arribas J. A role for a PDZ protein in the early secretory pathway for the targeting of proTGF-alpha to the cell surface. Mol Cell. 1999 Apr;3(4):423-33. PMID:10230395
↑ Zimmermann P, Tomatis D, Rosas M, Grootjans J, Leenaerts I, Degeest G, Reekmans G, Coomans C, David G. Characterization of syntenin, a syndecan-binding PDZ protein, as a component of cell adhesion sites and microfilaments. Mol Biol Cell. 2001 Feb;12(2):339-50. PMID:11179419
↑ Geijsen N, Uings IJ, Pals C, Armstrong J, McKinnon M, Raaijmakers JA, Lammers JW, Koenderman L, Coffer PJ. Cytokine-specific transcriptional regulation through an IL-5Ralpha interacting protein. Science. 2001 Aug 10;293(5532):1136-8. PMID:11498591 doi:http://dx.doi.org/10.1126/science.1059157
↑ Kang BS, Devedjiev Y, Derewenda U, Derewenda ZS. The PDZ2 domain of syntenin at ultra-high resolution: bridging the gap between macromolecular and small molecule crystallography. J Mol Biol. 2004 Apr 30;338(3):483-93. PMID:15081807 doi:http://dx.doi.org/10.1016/j.jmb.2004.02.057

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1r6j"

@@ Line 2: / Line 2: @@
 <StructureSection load='1r6j' size='340' side='right' caption='[[1r6j]], [[Resolution|resolution]] 0.73&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1r6j]] is a 1 chain structure with sequence 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=1R6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R6J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1r6j]] 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=1R6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1R6J FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SDCBP OR MDA9 OR SYCL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SDCBP OR MDA9 OR SYCL ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1r6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r6j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1r6j RCSB], [http://www.ebi.ac.uk/pdbsum/1r6j PDBsum]</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=1r6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r6j OCA], [http://pdbe.org/1r6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1r6j RCSB], [http://www.ebi.ac.uk/pdbsum/1r6j PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 27: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1r6j" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Homo sapiens]]
+[[Category: Human]]
 [[Category: Derewenda, U]]
 [[Category: Derewenda, Z S]]

1r6j

From Proteopedia

Revision as of 07:12, 10 September 2015

Ultrahigh resolution Crystal Structure of syntenin PDZ2

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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