3vi4: Difference between revisions

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-[[Image:3vi4.png|left|200px]]
-<!--
+==Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide==
-The line below this paragraph, containing "STRUCTURE_3vi4", creates the "Structure Box" on the page.
+<StructureSection load='3vi4' size='340' side='right'caption='[[3vi4]], [[Resolution|resolution]] 2.90&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'>[[3vi4]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VI4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VI4 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]] 2.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-{{STRUCTURE_3vi4|  PDB=3vi4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vi4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vi4 OCA], [https://pdbe.org/3vi4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vi4 RCSB], [https://www.ebi.ac.uk/pdbsum/3vi4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vi4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ITA5_HUMAN ITA5_HUMAN] Integrin alpha-5/beta-1 is a receptor for fibronectin and fibrinogen. It recognizes the sequence R-G-D in its ligands. In case of HIV-1 infection, the interaction with extracellular viral Tat protein seems to enhance angiogenesis in Kaposi's sarcoma lesions.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Integrin alpha5beta1 is a major cellular receptor for the extracellular matrix protein fibronectin and plays a fundamental role during mammalian development. A crystal structure of the alpha5beta1 integrin headpiece fragment bound by an allosteric inhibitory antibody was determined at a 2.9-A resolution both in the absence and presence of a ligand peptide containing the Arg-Gly-Asp (RGD) sequence. The antibody-bound beta1 chain accommodated the RGD ligand with very limited structural changes, which may represent the initial step of cell adhesion mediated by nonactivated integrins. Furthermore, a molecular dynamics simulation pointed to an important role for Ca(2+) in the conformational coupling between the ligand-binding site and the rest of the molecule. The RGD-binding pocket is situated at the center of a trenchlike exposed surface on the top face of alpha5beta1 devoid of glycosylation sites. The structure also enabled the precise prediction of the acceptor residue for the auxiliary synergy site of fibronectin on the alpha5 subunit, which was experimentally confirmed by mutagenesis and kinetic binding assays.
-===Crystal structure of alpha5beta1 integrin headpiece in complex with RGD peptide===
+Crystal structure of alpha5beta1 integrin ectodomain: Atomic details of the fibronectin receptor.,Nagae M, Re S, Mihara E, Nogi T, Sugita Y, Takagi J J Cell Biol. 2012 Apr 2;197(1):131-40. Epub 2012 Mar 26. PMID:22451694<ref>PMID:22451694</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3vi4" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_22451694}}, adds the Publication Abstract to the page
+*[[Integrin 3D structures|Integrin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 22451694 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22451694}}
+__TOC__
+</StructureSection>
-==About this Structure==
-[[3vi4]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VI4 OCA].
-==Reference==
-<ref group="xtra">PMID:022451694</ref><references group="xtra"/>
 [[Category: Homo sapiens]]
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Nagae, M.]]
+[[Category: Nagae M]]
-[[Category: Nogi, T.]]
+[[Category: Nogi T]]
-[[Category: Takagi, J.]]
+[[Category: Takagi J]]
-[[Category: Beta propeller fold]]
-[[Category: Beta sandwich]]
-[[Category: Cell adhesion-immune system complex]]
-[[Category: Fibronectin receptor]]
-[[Category: Rossman fold]]