2a6d: Difference between revisions

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-[[Image:2a6d.png|left|200px]]
-{{STRUCTURE_2a6d|  PDB=2a6d  |  SCENE=  }}
+==Crystal structure analysis of the anti-arsonate germline antibody 36-65 in complex with a phage display derived dodecapeptide RLLIADPPSPRE==
+<StructureSection load='2a6d' size='340' side='right'caption='[[2a6d]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2a6d]] is a 5 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=2A6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A6D 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]] 2.9&#8491;</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=2a6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a6d OCA], [https://pdbe.org/2a6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a6d RCSB], [https://www.ebi.ac.uk/pdbsum/2a6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a6d ProSAT]</span></td></tr>
+</table>
+== 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/a6/2a6d_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=2a6d ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Correlation between the promiscuity of the primary antibody response and conformational flexibility in a germline antibody was addressed by using germline antibody 36-65. Crystallographic analyses of the 36-65 Fab with three independent dodecapeptides provided mechanistic insights into the generation of antibody diversity. While four antigen-free Fab molecules provided a quantitative description of the conformational repertoire of the antibody CDRs, three Fab molecules bound to structurally diverse peptide epitopes exhibited a common paratope conformation. Each peptide revealed spatially different footprints within the antigen-combining site. However, a conformation-specific lock involving two shared residues, which were also associated with hapten binding, was discernible. Unlike the hapten, the peptides interacted with residues that undergo somatic mutations, suggesting a possible mechanism for excluding "nonspecific" antigens during affinity maturation. The observed multiple binding modes of diverse epitopes within a common paratope conformation of a germline antibody reveal a simple, yet elegant, mechanism for expanding the primary antibody repertoire.
-===Crystal structure analysis of the anti-arsonate germline antibody 36-65 in complex with a phage display derived dodecapeptide RLLIADPPSPRE===
+Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response.,Sethi DK, Agarwal A, Manivel V, Rao KV, Salunke DM Immunity. 2006 Apr;24(4):429-38. PMID:16618601<ref>PMID:16618601</ref>
-{{ABSTRACT_PUBMED_16618592}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2a6d" style="background-color:#fffaf0;"></div>
-[[2a6d]] is a 5 chain structure with 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=2A6D OCA].
 ==See Also==
-*[[Monoclonal Antibody|Monoclonal Antibody]]
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-==Reference==
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
-<ref group="xtra">PMID:016618592</ref><ref group="xtra">PMID:016618601</ref><references group="xtra"/>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Agarwal, A.]]
+[[Category: Agarwal A]]
-[[Category: Manivel, V.]]
+[[Category: Manivel V]]
-[[Category: Rao, K V.]]
+[[Category: Rao KV]]
-[[Category: Salunke, D M.]]
+[[Category: Salunke DM]]
-[[Category: Sethi, D K.]]
+[[Category: Sethi DK]]
-[[Category: Antibody]]
-[[Category: Fab]]
-[[Category: Germline]]
-[[Category: Immune system]]