2a6d
From Proteopedia
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==Crystal structure analysis of the anti-arsonate germline antibody 36-65 in complex with a phage display derived dodecapeptide RLLIADPPSPRE== | ==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]] 2.90Å' scene=''> | + | <StructureSection load='2a6d' size='340' side='right'caption='[[2a6d]], [[Resolution|resolution]] 2.90Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2a6d]] is a 5 chain structure with sequence from [ | + | <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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9Å</td></tr> |
| - | <table> | + | <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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a6/2a6d_consurf.spt"</scriptWhenChecked> | + | <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> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </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/ | + | </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="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == 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. | |
| - | + | 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> | |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
| + | <div class="pdbe-citations 2a6d" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
| - | *[[Antibody|Antibody]] | + | *[[Antibody 3D structures|Antibody 3D structures]] |
| - | *[[Monoclonal | + | *[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]] |
| + | *[[3D structures of non-human antibody|3D structures of non-human antibody]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
[[Category: Mus musculus]] | [[Category: Mus musculus]] | ||
| - | [[Category: Agarwal | + | [[Category: Agarwal A]] |
| - | [[Category: Manivel | + | [[Category: Manivel V]] |
| - | [[Category: Rao | + | [[Category: Rao KV]] |
| - | [[Category: Salunke | + | [[Category: Salunke DM]] |
| - | [[Category: Sethi | + | [[Category: Sethi DK]] |
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Current revision
Crystal structure analysis of the anti-arsonate germline antibody 36-65 in complex with a phage display derived dodecapeptide RLLIADPPSPRE
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Categories: Large Structures | Mus musculus | Agarwal A | Manivel V | Rao KV | Salunke DM | Sethi DK
