Crystal structure of the broadly cross-reactive HIV-1-neutralizing Fab X5 and fine mapping of its epitope

Biochemistry. 2004 Feb 17;43(6):1410-7. doi: 10.1021/bi035323x.


The human monoclonal antibody Fab X5 neutralizes a broad range of HIV-1 primary isolates. The crystal structure of X5 has been determined at 1.9 A resolution. There are two crystallographically independent Fab fragments in the asymmetric unit. The crystallographic R value for the final model is 0.22. The antibody-combining site features a long (22 amino acid residues) CDR H3 with a protruding hook-shaped motif. The X5 structure and site-directed mutagenesis data suggest that X5 amino acid residues W100 and Y100F in the CDR H3 motif may be critical for the binding of Fab X5 to gp120. X5 bound to a complex of a CD4 mimetic and gp120 with approximately the same kinetics and affinity as to a CD4-gp120 complex, suggesting that specific interactions between CD4 and X5 are unlikely to contribute to the binding of X5 to gp120-CD4 complexes. Binding of X5 to alanine scanning mutants of gp120JR-CSF complexed with CD4 suggested a critical role of the highly conserved amino acid residues at positions 423 and 432. The X5 structure and fine mapping of its epitope may assist in the elucidation of the mechanisms of viral entry and neutralization, and the development of HIV-1 inhibitors and vaccines.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Antibodies, Monoclonal / chemistry*
  • Antibodies, Monoclonal / genetics
  • Antibodies, Monoclonal / metabolism
  • Antiviral Agents / chemistry
  • Antiviral Agents / genetics
  • Antiviral Agents / metabolism
  • Binding Sites / genetics
  • CD4 Antigens / chemistry
  • CD4 Antigens / immunology
  • CD4 Antigens / metabolism
  • Cross Reactions / genetics
  • Crystallization
  • Crystallography, X-Ray
  • Epitopes / chemistry*
  • Epitopes / immunology*
  • Epitopes / metabolism
  • HIV Envelope Protein gp120 / chemistry
  • HIV Envelope Protein gp120 / genetics
  • HIV Envelope Protein gp120 / metabolism
  • HIV-1 / immunology*
  • HIV-1 / pathogenicity
  • Humans
  • Immunoglobulin Fab Fragments / chemistry*
  • Immunoglobulin Fab Fragments / genetics
  • Immunoglobulin Fab Fragments / metabolism
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Neutralization Tests
  • Peptide Mapping* / methods
  • Protein Structure, Tertiary / genetics
  • Surface Plasmon Resonance


  • Antibodies, Monoclonal
  • Antiviral Agents
  • CD4 Antigens
  • Epitopes
  • HIV Envelope Protein gp120
  • Immunoglobulin Fab Fragments

Associated data

  • PDB/1RHH