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3okn

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Revision as of 03:57, 10 December 2016

Crystal structure of S25-39 in complex with Kdo(2.4)Kdo(2.4)Kdo

Structural highlights

3okn is a 2 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	3okd, 3oke, 3okk, 3mhl, 3mhm, 3mho
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

The crystal structures of the antigen-binding fragment of the murine monoclonal antibody (mAb) S25-39 in the presence of several antigens representing chlamydial lipopolysaccharide (LPS) epitopes based on the bacterial sugar 3-deoxy-alpha-d-manno-oct-2-ulosonic acid (Kdo) have been determined at resolutions from 2.4 to 1.8 A. The antigen-binding site of this antibody differs from the well-characterized antibody S25-2 by a single mutation away from the germline of asparagine H53 to lysine, yet this one mutation results in a significant increase in avidity across a range of antigens. A comparison of the two antibody structures reveals that the mutated Lys H53 forms additional hydrogen bonds and/or charged-residue interactions with the second Kdo residue of every antigen having two or more carbohydrate residues. Significantly, the NH53K mutation results from a single nucleotide substitution in the germline sequence common among a panel of antibodies raised against glycoconjugates containing carbohydrate epitopes of chlamydial LPS. Like S25-2, S25-39 displays significant induced fit of complementarity determining region (CDR) H3 upon antigen binding, with the unliganded structure possessing a conformation distinct from those reported earlier for S25-2. The four different observed conformations for CDR H3 suggest that this CDR has evolved to exploit the recognition potential of a flexible loop while minimizing the associated entropic penalties of binding by adopting a limited number of ordered conformations in the unliganded state. These observations reveal strategies evolved to balance adaptability and specificity in the germline antibody response to carbohydrate antigens.

A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity.,Blackler RJ, Muller-Loennies S, Brooks CL, Evans DW, Brade L, Kosma P, Brade H, Evans SV Biochemistry. 2011 Apr 1. PMID:21405106^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Blackler RJ, Muller-Loennies S, Brooks CL, Evans DW, Brade L, Kosma P, Brade H, Evans SV. A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity. Biochemistry. 2011 Apr 1. PMID:21405106 doi:10.1021/bi101886v

1 Structural highlights
2 Publication Abstract from PubMed
3 See Also
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3okn"

@@ Line 1: / Line 1: @@
 ==Crystal structure of S25-39 in complex with Kdo(2.4)Kdo(2.4)Kdo==
 <StructureSection load='3okn' size='340' side='right' caption='[[3okn]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=KDA:(3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID)-2-O-ALLYL'>KDA</scene>, <scene name='pdbligand=KDO:3-DEOXY-D-MANNO-OCT-2-ULOSONIC+ACID'>KDO</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3okd|3okd]], [[3oke|3oke]], [[3okk|3okk]], [[3mhl|3mhl]], [[3mhm|3mhm]], [[3mho|3mho]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3okn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okn OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3okn RCSB], [http://www.ebi.ac.uk/pdbsum/3okn PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3okn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3okn OCA], [http://pdbe.org/3okn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3okn RCSB], [http://www.ebi.ac.uk/pdbsum/3okn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3okn ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 15: / Line 16: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3okn" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Antibody|Antibody]]
+*[[3D structures of antibody|3D structures of antibody]]
 == References ==
 <references/>

3okn

From Proteopedia

Revision as of 03:57, 10 December 2016

Crystal structure of S25-39 in complex with Kdo(2.4)Kdo(2.4)Kdo

Structural highlights

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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