This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1ybo

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of the PDZ tandem of human syntenin with syndecan peptide

Structural highlights

1ybo is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

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.

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^[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
↑ Grembecka J, Cierpicki T, Devedjiev Y, Derewenda U, Kang BS, Bushweller JH, Derewenda ZS. The binding of the PDZ tandem of syntenin to target proteins. Biochemistry. 2006 Mar 21;45(11):3674-83. PMID:16533050 doi:10.1021/bi052225y

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
 ==Crystal structure of the PDZ tandem of human syntenin with syndecan peptide==
-<StructureSection load='1ybo' size='340' side='right' caption='[[1ybo]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='1ybo' size='340' side='right'caption='[[1ybo]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ybo]] is a 4 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=1YBO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YBO FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ybo]] 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=1YBO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YBO FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SDCBP, MDA9, SYCL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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]] 2.3&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ybo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ybo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ybo RCSB], [http://www.ebi.ac.uk/pdbsum/1ybo 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=1ybo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ybo OCA], [https://pdbe.org/1ybo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ybo RCSB], [https://www.ebi.ac.uk/pdbsum/1ybo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ybo ProSAT]</span></td></tr>
-<table>
+</table>
+== 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/yb/1ybo_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yb/1ybo_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=1ybo ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1ybo" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Syntenin|Syntenin]]
+*[[3D structures of syntenin|3D structures of syntenin]]
 == References ==
 <references/>
@@ Line 29: / Line 37: @@
 </StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Cierpicki, T.]]
+[[Category: Large Structures]]
-[[Category: Cooper, D R.]]
+[[Category: Cierpicki T]]
-[[Category: Derewenda, Z.]]
+[[Category: Cooper DR]]
-[[Category: Devedjiev, Y.]]
+[[Category: Derewenda Z]]
-[[Category: Grembecka, J.]]
+[[Category: Devedjiev Y]]
-[[Category: Kang, B S.]]
+[[Category: Grembecka J]]
-[[Category: Adhesion complex]]
+[[Category: Kang BS]]
-[[Category: Pdz domain]]
-[[Category: Scaffolding protein]]
-[[Category: Structural protein]]

1ybo

From Proteopedia

Current revision

Crystal structure of the PDZ tandem of human syntenin with syndecan peptide

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox