1vdf

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[[Image:1vdf.gif|left|200px]]
 
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==ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN==
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The line below this paragraph, containing "STRUCTURE_1vdf", creates the "Structure Box" on the page.
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<StructureSection load='1vdf' size='340' side='right'caption='[[1vdf]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1vdf]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VDF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VDF FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.05&#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=CL:CHLORIDE+ION'>CL</scene></td></tr>
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{{STRUCTURE_1vdf| PDB=1vdf | SCENE= }}
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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=1vdf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vdf OCA], [https://pdbe.org/1vdf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vdf RCSB], [https://www.ebi.ac.uk/pdbsum/1vdf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vdf ProSAT]</span></td></tr>
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</table>
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'''ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN'''
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== Function ==
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[https://www.uniprot.org/uniprot/COMP_RAT COMP_RAT] May play a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as the collagens and fibronectin. Can mediate the interaction of chondrocytes with the cartilage extracellular matrix through interaction with cell surface integrin receptors. Could play a role in the pathogenesis of osteoarthritis. Potent suppressor of apoptosis in both primary chondrocytes and transformed cells. Suppresses apoptosis by blocking the activation of caspase-3 and by inducing the IAP family of survival proteins (BIRC3, BIRC2, BIRC5 and XIAP) (By similarity). Essential for maintaining a vascular smooth muscle cells (VSMCs) contractile/differentiated phenotype under physiological and pathological stimuli. Maintains this phenotype of VSMCs by interacting with ITGA7.
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== Evolutionary Conservation ==
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==Overview==
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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/vd/1vdf_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1vdf 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 ==
Oligomerization by the formation of alpha-helical bundles is common in many proteins. The crystal structure of a parallel pentameric coiled coil, constituting the oligomerization domain in the cartilage oligomeric matrix protein (COMP), was determined at 2.05 angstroms resolution. The same structure probably occurs in two other extracellular matrix proteins, thrombospondins 3 and 4. Complementary hydrophobic interactions and conserved disulfide bridges between the alpha helices result in a thermostable structure with unusual properties. The long hydrophobic axial pore is filled with water molecules but can also accommodate small apolar groups. An "ion trap" is formed inside the pore by a ring of conserved glutamines, which binds chloride and probably other monatomic anions. The oligomerization domain of COMP has marked similarities with proposed models of the pentameric transmembrane ion channels in phospholamban and the acetylcholine receptor.
Oligomerization by the formation of alpha-helical bundles is common in many proteins. The crystal structure of a parallel pentameric coiled coil, constituting the oligomerization domain in the cartilage oligomeric matrix protein (COMP), was determined at 2.05 angstroms resolution. The same structure probably occurs in two other extracellular matrix proteins, thrombospondins 3 and 4. Complementary hydrophobic interactions and conserved disulfide bridges between the alpha helices result in a thermostable structure with unusual properties. The long hydrophobic axial pore is filled with water molecules but can also accommodate small apolar groups. An "ion trap" is formed inside the pore by a ring of conserved glutamines, which binds chloride and probably other monatomic anions. The oligomerization domain of COMP has marked similarities with proposed models of the pentameric transmembrane ion channels in phospholamban and the acetylcholine receptor.
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==About this Structure==
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The crystal structure of a five-stranded coiled coil in COMP: a prototype ion channel?,Malashkevich VN, Kammerer RA, Efimov VP, Schulthess T, Engel J Science. 1996 Nov 1;274(5288):761-5. PMID:8864111<ref>PMID:8864111</ref>
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1VDF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VDF 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 crystal structure of a five-stranded coiled coil in COMP: a prototype ion channel?, Malashkevich VN, Kammerer RA, Efimov VP, Schulthess T, Engel J, Science. 1996 Nov 1;274(5288):761-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8864111 8864111]
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</div>
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<div class="pdbe-citations 1vdf" style="background-color:#fffaf0;"></div>
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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: Large Structures]]
[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Single protein]]
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[[Category: Malashkevich VN]]
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[[Category: Malashkevich, V N.]]
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[[Category: Assembly domain]]
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[[Category: Cartilage]]
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[[Category: Extracellular matrix protein]]
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[[Category: Glycoprotein]]
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[[Category: Oligomeric matrix protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 12:24:29 2008''
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Current revision

ASSEMBLY DOMAIN OF CARTILAGE OLIGOMERIC MATRIX PROTEIN

PDB ID 1vdf

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