4M93

Unliganded 2 crystal structure of S25-26 Fab

Summary for 4M93

• Entry DOI: 10.2210/pdb4m93/pdb
• Related: 4M7J 4M7Z 4MA1
• Descriptor: S25-26 Fab (IgG1k) light chain, S25-26 Fab (IgG1k) heavy chain, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (6 entities in total)
• Functional Keywords: carbohydrate/sugar binding, immune system
• Biological source: Mus musculus (mouse); More
• Total number of polymer chains: 4
• Total formula weight: 96168.47

Authors

Haji-Ghassemi, O.,Evans, S.V. (deposition date: 2013-08-14, release date: 2014-04-09, Last modification date: 2024-10-30)

Primary citation

Haji-Ghassemi, O.,Muller-Loennies, S.,Saldova, R.,Muniyappa, M.,Brade, L.,Rudd, P.M.,Harvey, D.J.,Kosma, P.,Brade, H.,Evans, S.V.
Groove-type Recognition of Chlamydiaceae-specific Lipopolysaccharide Antigen by a Family of Antibodies Possessing an Unusual Variable Heavy Chain N-Linked Glycan.
J.Biol.Chem., 289:16644-16661, 2014

PubMed Abstract: The structure of the antigen binding fragment of mAb S25-26, determined to 1.95 Å resolution in complex with the Chlamydiaceae family-specific trisaccharide antigen Kdo(2→8)Kdo(2→4)Kdo (Kdo = 3-deoxy-α-d-manno-oct-2-ulopyranosonic acid), displays a germ-line-coded paratope that differs significantly from previously characterized Chlamydiaceae-specific mAbs despite being raised against the identical immunogen. Unlike the terminal Kdo recognition pocket that promotes cross-reactivity in S25-2-type antibodies, S25-26 and the closely related S25-23 utilize a groove composed of germ-line residues to recognize the entire trisaccharide antigen and so confer strict specificity. Interest in S25-23 was sparked by its rare high μm affinity and strict specificity for the family-specific trisaccharide antigen; however, only the related antibody S25-26 proved amenable to crystallization. The structures of three unliganded forms of S25-26 have a labile complementary-determining region H3 adjacent to significant glycosylation of the variable heavy chain on asparagine 85 in Framework Region 3. Analysis of the glycan reveals a heterogeneous mixture with a common root structure that contains an unusually high number of terminal αGal-Gal moieties. One of the few reported structures of glycosylated mAbs containing these epitopes is the therapeutic antibody Cetuximab; however, unlike Cetuximab, one of the unliganded structures in S25-26 shows significant order in the glycan with appropriate electron density for nine residues. The elucidation of the three-dimensional structure of an αGal-containing N-linked glycan on a mAb variable heavy chain has potential clinical interest, as it has been implicated in allergic response in patients receiving therapeutic antibodies.

PubMed: 24682362
DOI: 10.1074/jbc.M113.528224

Experimental method

X-RAY DIFFRACTION (2.09 Å)