PDBsum entry 1qkz

Immune system

PDB id: 1qkz

Contents

Protein chains

58 a.a. *

219 a.a. *

214 a.a. *

Ligands

ALA-ASN-GLY-GLY-ALA-SER-GLY-GLN-VAL-LYS

Waters ×526

* Residue conservation analysis

PDB id:

1qkz

Name:

Immune system

Title:

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

Structure:

Protein g-prime. Chain: a. Fragment: domain ii. Engineered: yes. Mutation: yes. Antibody. Chain: h. Fragment: fab. Antibody.

Source:

Streptococcus sp.. Organism_taxid: 1320. Strain: group g. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. Mouse. Organism_taxid: 10090. Cell_line: mn14c11.6 murine hybridoma.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.95Å R-factor: 0.209 R-free: 0.262

Authors:

J.P.Derrick,I.Feavers,M.C.J.Maiden

Key ref:

J.P.Derrick et al. (1999). Crystal structure of an Fab fragment in complex with a meningococcal serosubtype antigen and a protein G domain. J Mol Biol, 293, 81-91. PubMed id: 10512717 DOI: 10.1006/jmbi.1999.3144

Date:

17-Aug-99 Release date: 06-Feb-00

Protein chain

P19909  (SPG2_STRSG) -  Immunoglobulin G-binding protein G from Streptococcus sp. group G

Seq: 593 a.a.

Struc: 58 a.a.*

Protein chain

No UniProt id for this chain

Struc: 219 a.a.

Protein chain

No UniProt id for this chain

Struc: 214 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1006/jmbi.1999.3144

J Mol Biol 293:81-91 (1999)

PubMed id: 10512717

Crystal structure of an Fab fragment in complex with a meningococcal serosubtype antigen and a protein G domain.

J.P.Derrick, M.C.Maiden, I.M.Feavers.

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.

Selected figure(s)

Figure 5.
Figure 5. View of the peptide within the antigen bind- ing site, prepared using the program GRASP (Nicholls et al., 1991)). The molecular surface of the antigen bind- ing site is displayed and coloured for electrostatic poten- tial: red for negative nd the blue for positive. The peptide is shown superimposed on top of the surface, colour coded by atom type (N, blue; O, red; and C, white).

Figure 6.
Figure 6. Stereo views of the peptide antigen and interacting residues from the Fab. (a) View of selected Fab residues involved in recognition of the C-terminal portion of the peptide antigen. (b) View of selected Fab residues involved in recognition of the b-turn within the peptide antigen.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 293, 81-91) copyright 1999.

Figures were selected by the author.