1QKZ

Fab fragment (MN14C11.6) in complex with a peptide antigen derived from Neisseria meningitidis P1.7 serosubtype antigen and domain II from Streptococcal protein G

Summary for 1QKZ

• Entry DOI: 10.2210/pdb1qkz/pdb
• Descriptor: PROTEIN G-PRIME, ANTIBODY, MAJOR OUTER MEMBRANE PROTEIN P1.16, ... (5 entities in total)
• Functional Keywords: immune system, fab, pora, neisseria meningitidis, porin
• Biological source: STREPTOCOCCUS SP.; More
• Total number of polymer chains: 4
• Total formula weight: 55611.86

Authors

Derrick, J.P.,Feavers, I.,Maiden, M.C.J. (deposition date: 1999-08-17, release date: 2000-02-06, Last modification date: 2023-12-13)

Primary citation

Derrick, J.P.,Feavers, I.M.,Maiden, M.C.J.
Crystal Structure of an Fab Fragment in Complex with a Meningococcal Serosubtype Antigen and a Protein G Domain
J.Mol.Biol., 293:81-, 1999

PubMed Abstract: Many pathogens present highly variable surface proteins to their host as a means of evading immune responses. The structure of a peptide antigen corresponding to the subtype P1.7 variant of the porin PorA from the human pathogen Neisseria meningitidis was determined by solution of the X-ray crystal structure of the ternary complex of the peptide (ANGGASGQVK) in complex with a Fab fragment and a domain from streptococcal protein G to 1.95 A resolution. The peptide adopted a beta-hairpin structure with a type I beta-turn between residues Gly4P and Gly7P, the conformation of the peptide being further stabilised by a pair of hydrogen bonds from the side-chain of Asn2P to main-chain atoms in Val9P. The antigen binding site within the Fab formed a distinct crevice lined by a high proportion of apolar amino acids. Recognition was supplemented by hydrogen bonds from heavy chain residues Thr50H, Asp95H, Leu97H and Tyr100H to main-chain and side-chain atoms in the peptide. Complementarity-determining region (CDR) 3 of the heavy chain was responsible for approximately 50 % of the buried surface area formed by peptide-Fab binding, with the remainder made up from CDRs 1 and 3 of the light chain and CDRs 1 and 2 of the heavy chain. Knowledge of the structures of variable surface antigens such as PorA is an essential prerequisite to a molecular understanding of antigenic variation and its implications for vaccine design.

PubMed: 10512717
DOI: 10.1006/JMBI.1999.3144

Experimental method

X-RAY DIFFRACTION (1.95 Å)