2J5L

Structure of a Plasmodium falciparum apical membrane antigen 1-Fab F8. 12.19 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Cross-Reactivity Studies of an Anti-Plasmodium Vivax Apical Membrane Antigen 1 Monoclonal Antibody: Binding and Structural Characterisation.

Igonet, S.Vulliez-Le Normand, B.Faure, G.Riottot, M.M.Kocken, C.H.M.Thomas, A.W.Bentley, G.A.

(2007) J.Mol.Biol. 366: 1523

  • DOI: 10.1016/j.jmb.2006.12.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Apical membrane antigen 1 (AMA1) has an important, but as yet uncharacterised, role in host cell invasion by the malaria parasite, Plasmodium. The protein, which is quite conserved between Plasmodium species, comprises an ectoplasmic region, a single ...

    Apical membrane antigen 1 (AMA1) has an important, but as yet uncharacterised, role in host cell invasion by the malaria parasite, Plasmodium. The protein, which is quite conserved between Plasmodium species, comprises an ectoplasmic region, a single transmembrane segment and a small cytoplasmic domain. The ectoplasmic region, which can induce protective immunity in animal models of human malaria, is a leading vaccine candidate that has entered clinical trials. The monoclonal antibody F8.12.19, raised against the recombinant ectoplasmic region of AMA1 from Plasmodium vivax, cross-reacts with homologues from Plasmodium knowlesi, Plasmodium cynomolgi, Plasmodium berghei and Plasmodium falciparum, as shown by immunofluorescence assays on mature schizonts. The binding of F8.12.19 to recombinant AMA1 from both P. vivax and P. falciparum was measured by surface plasmon resonance, revealing an apparent affinity constant that is about 100-fold weaker for the cross-reacting antigen when compared to the cognate antigen. Crystal structure analysis of Fab F8.12.19 complexed to AMA1 from P. vivax and P. falciparum shows that the monoclonal antibody recognises a discontinuous epitope located on domain III of the ectoplasmic region, the major component being a loop containing a cystine knot. The structures provide a basis for understanding the cross-reactivity. Antibody contacts are made mainly to main-chain and invariant side-chain atoms of AMA1; contact antigen residues that differ in sequence are located at the periphery of the antigen-binding site and can be accommodated at the interface between the two components of the complex. The implications for AMA1 vaccine development are discussed.


    Organizational Affiliation

    Unité d'Immunologie Structurale, CNRS URA 2185, Département de Biologie Structurale et Chimie, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris cedex 15, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APICAL MEMBRANE ANTIGEN 1
A
581Plasmodium falciparumMutation(s): 1 
Gene Names: ama-1
Find proteins for Q9BIM8 (Plasmodium falciparum)
Go to UniProtKB:  Q9BIM8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19
B
213Mus musculusMutation(s): 0 
Find proteins for Q5XFY8 (Mus musculus)
Go to UniProtKB:  Q5XFY8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19
C
225N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
B
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.212 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 171.900α = 90.00
b = 171.900β = 90.00
c = 44.200γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
AMoREphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance