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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of an Fab Fragment in Complex with a Meningococcal Serosubtype Antigen and a Protein G Domain

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

(1999) J.Mol.Biol. 293: 81

  • DOI: 10.1006/jmbi.1999.3144

  • 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 meningitidi ...

    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.


    Organizational Affiliation

    Department of Biomolecular Sciences, UMIST, Manchester, M60 1QD, UK. Jeremy.Derrick@umist.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN G-PRIME
A
64Streptococcus sp. group GMutation(s): 1 
Gene Names: spg
Find proteins for P19909 (Streptococcus sp. group G)
Go to UniProtKB:  P19909
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY
H
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ANTIBODY
L
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
MAJOR OUTER MEMBRANE PROTEIN P1.16
P
10Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)Mutation(s): 0 
Gene Names: porA
Find proteins for P57041 (Neisseria meningitidis serogroup A / serotype 4A (strain Z2491))
Go to UniProtKB:  P57041
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 43.482α = 90.00
b = 63.099β = 81.54
c = 89.374γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
AMoREphasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-02-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance