3OKD

Crystal structure of S25-39 in complex with Kdo

Summary for 3OKD

• Entry DOI: 10.2210/pdb3okd/pdb
• Related: 3MHL 3MHM 3MHN 3MHO 3OKE 3OKK
• Descriptor: S25-39 Fab (IgG1k) light chain, S25-39 Fab (IgG1k) heavy chain, DI(HYDROXYETHYL)ETHER, ... (6 entities in total)
• Functional Keywords: antibody, fab, igg, carbohydrate, immune system
• Biological source: Mus musculus; More
• Total number of polymer chains: 2
• Total formula weight: 48635.53

Authors

Blackler, R.J.,Evans, S.V. (deposition date: 2010-08-24, release date: 2011-04-06, Last modification date: 2020-07-29)

Primary citation

Blackler, R.J.,Brooks, C.L.,Evans, D.W.,Brade, L.,Kosma, P.,Brade, H.,Evans, S.V.
A Common NH53K Mutation in the Combining Site of Antibodies Raised against Chlamydial LPS Glycoconjugates Significantly Increases Avidity.
Biochemistry, 50:3357-3368, 2011

PubMed Abstract: 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-α-D-manno-oct-2-ulosonic acid (Kdo) have been determined at resolutions from 2.4 to 1.8 Å. 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.

PubMed: 21405106
DOI: 10.1021/bi101886v

Experimental method

X-RAY DIFFRACTION (1.8 Å)