3ghb: Difference between revisions

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-[[Image:3ghb.png|left|200px]]
-{{STRUCTURE_3ghb|  PDB=3ghb  |  SCENE=  }}
+==Crystal structure of anti-HIV-1 Fab 447-52D in complex with V3 peptide W2RW020==
+<StructureSection load='3ghb' size='340' side='right'caption='[[3ghb]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3ghb]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GHB FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=3ghb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ghb OCA], [https://pdbe.org/3ghb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ghb RCSB], [https://www.ebi.ac.uk/pdbsum/3ghb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ghb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/P88213_9HIV1 P88213_9HIV1]
+== 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/gh/3ghb_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=3ghb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Human monoclonal antibodies 447-52D and 537-10D, both coded by the VH3 gene and specific for the third variable region (V3) of the HIV-1 gp120, were found to share antigen-binding structural elements including an elongated CDR H3 forming main-chain interactions with the N terminus of the V3 crown. However, water-mediated hydrogen bonds and a unique cation-pi sandwich stacking allow 447-52D to be broadly reactive with V3 containing both the GPGR and GPGQ crown motifs, while the deeper binding pocket and a buried Glu in the binding site of 537-10D limit its reactivity to only V3 containing the GPGR motif. Our results suggest that the design of immunogens for anti-V3 antibodies should avoid the Arg at the V3 crown, as GPGR-containing epitopes appear to select for B cells making antibodies of narrower specificity than V3 that carry Gln at this position.
-===Crystal structure of anti-HIV-1 Fab 447-52D in complex with V3 peptide W2RW020===
+Structural basis of the cross-reactivity of genetically related human anti-HIV-1 mAbs: implications for design of V3-based immunogens.,Burke V, Williams C, Sukumaran M, Kim SS, Li H, Wang XH, Gorny MK, Zolla-Pazner S, Kong XP Structure. 2009 Nov 11;17(11):1538-46. PMID:19913488<ref>PMID:19913488</ref>
-{{ABSTRACT_PUBMED_19913488}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3ghb" style="background-color:#fffaf0;"></div>
-[[3ghb]] is a 6 chain structure of [[Antibody]] 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=3GHB OCA].
 ==See Also==
-*[[Antibody|Antibody]]
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[3D structures of human antibody|3D structures of human antibody]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:019913488</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Burke, V J.]]
+[[Category: Human immunodeficiency virus 1]]
-[[Category: Kong, X P.]]
+[[Category: Large Structures]]
-[[Category: Antibody-antigen interaction]]
+[[Category: Burke VJ]]
-[[Category: Envelope protein]]
+[[Category: Kong XP]]
-[[Category: Hiv]]
-[[Category: Immune system]]
-[[Category: V3 loop]]