2wuh: Difference between revisions

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-[[Image:2wuh.png|left|200px]]
-<!--
+==Crystal structure of the DDR2 discoidin domain bound to a triple- helical collagen peptide==
-The line below this paragraph, containing "STRUCTURE_2wuh", creates the "Structure Box" on the page.
+<StructureSection load='2wuh' size='340' side='right'caption='[[2wuh]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2wuh]] 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=2WUH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WUH FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=NLE:NORLEUCINE'>NLE</scene></td></tr>
-{{STRUCTURE_2wuh|  PDB=2wuh  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2wuh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wuh OCA], [https://pdbe.org/2wuh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wuh RCSB], [https://www.ebi.ac.uk/pdbsum/2wuh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wuh ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN] Defects in DDR2 are the cause of spondyloepimetaphyseal dysplasia short limb-hand type (SEMD-SL) [MIM:[https://omim.org/entry/271665 271665]. A bone disease characterized by short-limbed dwarfism, a narrow chest with pectus excavatum, brachydactyly in the hands and feet, a characteristic craniofacial appearance and premature calcifications. The radiological findings are distinctive and comprise short long bones throughout the skeleton with striking epiphyses that are stippled, flattened and fragmented and flared, irregular metaphyses. Platyspondyly in the spine with wide intervertebral spaces is observed and some vertebral bodies are pear-shaped with central humps, anterior protrusions and posterior scalloping.<ref>PMID:20223752</ref> <ref>PMID:19110212</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/DDR2_HUMAN DDR2_HUMAN] Tyrosine kinase that functions as cell surface receptor for fibrillar collagen and regulates cell differentiation, remodeling of the extracellular matrix, cell migration and cell proliferation. Required for normal bone development. Regulates osteoblast differentiation and chondrocyte maturation via a signaling pathway that involves MAP kinases and leads to the activation of the transcription factor RUNX2. Regulates remodeling of the extracellular matrix by up-regulation of the collagenases MMP1, MMP2 and MMP13, and thereby facilitates cell migration and tumor cell invasion. Promotes fibroblast migration and proliferation, and thereby contributes to cutaneous wound healing.<ref>PMID:9659899</ref> <ref>PMID:16186108</ref> <ref>PMID:16186104</ref> <ref>PMID:17665456</ref> <ref>PMID:18201965</ref> <ref>PMID:20564243</ref> <ref>PMID:20734453</ref> <ref>PMID:20004161</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/wu/2wuh_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=2wuh ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The discoidin domain receptors, DDR1 and DDR2, are widely expressed receptor tyrosine kinases that are activated by triple-helical collagen. They control important aspects of cell behavior and are dysregulated in several human diseases. The major DDR2-binding site in collagens I-III is a GVMGFO motif (O is hydroxyproline) that also binds the matricellular protein SPARC. We have determined the crystal structure of the discoidin domain of human DDR2 bound to a triple-helical collagen peptide. The GVMGFO motifs of two collagen chains are recognized by an amphiphilic pocket delimited by a functionally critical tryptophan residue and a buried salt bridge. Collagen binding results in structural changes of DDR2 surface loops that may be linked to the process of receptor activation. A comparison of the GVMGFO-binding sites of DDR2 and SPARC reveals a striking case of convergent evolution in collagen recognition.
-===CRYSTAL STRUCTURE OF THE DDR2 DISCOIDIN DOMAIN BOUND TO A TRIPLE-HELICAL COLLAGEN PEPTIDE===
+Crystallographic insight into collagen recognition by discoidin domain receptor 2.,Carafoli F, Bihan D, Stathopoulos S, Konitsiotis AD, Kvansakul M, Farndale RW, Leitinger B, Hohenester E Structure. 2009 Dec 9;17(12):1573-81. PMID:20004161<ref>PMID:20004161</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2wuh" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20004161}}, adds the Publication Abstract to the page
+*[[Collagen 3D structures|Collagen 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20004161 is the PubMed ID number.
+*[[Epithelial discoidin domain-containing receptor|Epithelial discoidin domain-containing receptor]]
--->
+== References ==
-{{ABSTRACT_PUBMED_20004161}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-[[2wuh]] 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=2WUH OCA].
-==Reference==
-<ref group="xtra">PMID:20004161</ref><ref group="xtra">PMID:17703188</ref><ref group="xtra">PMID:18201965</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
-[[Category: Bihan, D.]]
+[[Category: Large Structures]]
-[[Category: Carafoli, F.]]
+[[Category: Bihan D]]
-[[Category: Farndale, R W.]]
+[[Category: Carafoli F]]
-[[Category: Hohenester, E.]]
+[[Category: Farndale RW]]
-[[Category: Konitsiotis, A D.]]
+[[Category: Hohenester E]]
-[[Category: Kvansakul, M.]]
+[[Category: Konitsiotis AD]]
-[[Category: Leitinger, B.]]
+[[Category: Kvansakul M]]
-[[Category: Stathopoulos, S.]]
+[[Category: Leitinger B]]
-[[Category: Nucleotide-binding]]
+[[Category: Stathopoulos S]]
-[[Category: Receptor-peptide complex]]
-[[Category: Transferase]]
-[[Category: Tyrosine-protein kinase]]