2fat: Difference between revisions

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-[[Image:2fat.gif|left|200px]]
- {{Structure
+==An anti-urokinase plasminogen activator receptor (UPAR) antibody: Crystal structure and binding epitope==
-|PDB= 2fat |SIZE=350|CAPTION= <scene name='initialview01'>2fat</scene>, resolution 1.77&Aring;
+<StructureSection load='2fat' size='340' side='right'caption='[[2fat]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND=
+<table><tr><td colspan='2'>[[2fat]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FAT FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.77&#8491;</td></tr>
-|GENE=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2fat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fat OCA], [https://pdbe.org/2fat PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fat RCSB], [https://www.ebi.ac.uk/pdbsum/2fat PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fat ProSAT]</span></td></tr>
-|DOMAIN=
+</table>
-|RELATEDENTRY=
+== Evolutionary Conservation ==
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fat FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fat OCA], [http://www.ebi.ac.uk/pdbsum/2fat PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2fat RCSB]</span>
+[[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/fa/2fat_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2fat ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Human urokinase-type plasminogen activator receptor (uPAR/CD87) is expressed at the invasive interface of the tumor-stromal microenvironment in many human cancers and interacts with a wide array of extracellular molecules. An anti-uPAR antibody (ATN615) was prepared using hybridoma technology. This antibody binds to uPAR in vitro with high affinity (K(d) approximately 1 nM) and does not interfere with uPA binding to uPAR. Here we report the crystal structure of the Fab fragment of ATN615 at 1.77 A and the analysis of ATN615-suPAR-ATF structure that was previously determined, emphasizing the ATN615-suPAR interaction. The complementarity determining regions (CDRs) of ATN615 consist of a high percentage of aromatic residues, and form a relatively flat and undulating surface. The ATN615 Fab fragment recognizes domain 3 of suPAR. The antibody-antigen recognition involves 11 suPAR residues and 12 Fab residues from five CDRs. Structural data suggest that Pro188, Asn190, Gly191, and Arg192 residues of uPAR are the key residues for the antibody recognition, while Pro189 and Arg192 render specificity of ATN615 for human uPAR. Interestingly, this antibody-antigen interface has a small contact area, mainly polar interaction with little hydrophobic character, yet has high binding strength. Furthermore, several solvent molecules (assigned as polyethylene glycols) were clearly visible in the binding interface between antibody and antigen, suggesting that solvent molecules may be important for the maximal binding between suPAR and ATN615 Fab. ATN615 undergoes small but noticeable changes in its CDR region upon antigen binding.
-'''An anti-urokinase plasminogen activator receptor (UPAR) antibody: Crystal structure and binding epitope'''
+An anti-urokinase plasminogen activator receptor (uPAR) antibody: crystal structure and binding epitope.,Li Y, Parry G, Chen L, Callahan JA, Shaw DE, Meehan EJ, Mazar AP, Huang M J Mol Biol. 2007 Jan 26;365(4):1117-29. Epub 2006 Oct 21. PMID:17101149<ref>PMID:17101149</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2fat" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Human urokinase-type plasminogen activator receptor (uPAR/CD87) is expressed at the invasive interface of the tumor-stromal microenvironment in many human cancers and interacts with a wide array of extracellular molecules. An anti-uPAR antibody (ATN615) was prepared using hybridoma technology. This antibody binds to uPAR in vitro with high affinity (K(d) approximately 1 nM) and does not interfere with uPA binding to uPAR. Here we report the crystal structure of the Fab fragment of ATN615 at 1.77 A and the analysis of ATN615-suPAR-ATF structure that was previously determined, emphasizing the ATN615-suPAR interaction. The complementarity determining regions (CDRs) of ATN615 consist of a high percentage of aromatic residues, and form a relatively flat and undulating surface. The ATN615 Fab fragment recognizes domain 3 of suPAR. The antibody-antigen recognition involves 11 suPAR residues and 12 Fab residues from five CDRs. Structural data suggest that Pro188, Asn190, Gly191, and Arg192 residues of uPAR are the key residues for the antibody recognition, while Pro189 and Arg192 render specificity of ATN615 for human uPAR. Interestingly, this antibody-antigen interface has a small contact area, mainly polar interaction with little hydrophobic character, yet has high binding strength. Furthermore, several solvent molecules (assigned as polyethylene glycols) were clearly visible in the binding interface between antibody and antigen, suggesting that solvent molecules may be important for the maximal binding between suPAR and ATN615 Fab. ATN615 undergoes small but noticeable changes in its CDR region upon antigen binding.
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[Sandbox 20009|Sandbox 20009]]
-==About this Structure==
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
-FAT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FAT OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-An anti-urokinase plasminogen activator receptor (uPAR) antibody: crystal structure and binding epitope., Li Y, Parry G, Chen L, Callahan JA, Shaw DE, Meehan EJ, Mazar AP, Huang M, J Mol Biol. 2007 Jan 26;365(4):1117-29. Epub 2006 Oct 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17101149 17101149]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Callahan JA]]
-[[Category: Callahan, J A.]]
+[[Category: Chen L]]
-[[Category: Chen, L.]]
+[[Category: Huang M]]
-[[Category: Huang, M.]]
+[[Category: Li Y]]
-[[Category: Li, Y.]]
+[[Category: Mazar AP]]
-[[Category: Mazar, A P.]]
+[[Category: Parry G]]
-[[Category: Parry, G.]]
+[[Category: Shi X]]
-[[Category: Shi, X.]]
-[[Category: anti-upar antibody]]
-[[Category: atn-615]]
-[[Category: crystal structure]]
-[[Category: fab]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:00:12 2008''