Crystal structure of the complex between the F(ab)' fragment of the cross-neutralizing anti-HIV-1 antibody 2F5 and the F(ab) fragment of its anti-idiotypic antibody 3H6

J Mol Biol. 2008 Oct 17;382(4):910-9. doi: 10.1016/j.jmb.2008.07.057. Epub 2008 Jul 27.

Abstract

The monoclonal antibody 2F5 neutralizes a broad range of human immunodeficiency virus-1 isolates via a conserved epitope on the viral glycoprotein gp41. The conformation of the principal epitope is a type I beta-turn centered on gp41 residues (664)DKW(666); in addition, binding studies indicate that residues N- and C-terminal to this core as well as structurally more distant parts of gp41 also contribute to the interaction. Ab2/3H6 is an anti-idiotypic antibody that inhibits the interaction between 2F5 and gp41 and as such, Ab2/3H6 may, in principle, possess a paratope that mimics the gp41 epitope. To establish the potential of Ab2/3H6 to serve as a guide for the design of vaccine components against human immunodeficiency virus, we investigated the crystal structure of the heterodimeric complex of Ab2/3H6 F(ab) and 2F5 F(ab)'. Ab2/3H6 F(ab) binds to 2F5 F(ab)' via a helix-like protrusion formed by residues (58(H))RYSPSLNTRL(67(H)) of the 2F5 F(ab)' variable domain and proximal to but not overlapping with the gp41 (664)DKW(666) epitope-binding pocket. This defines Ab2/3H6 as an anti-idiotypic antibody of the Ab2gamma class, i.e., an antigen-inhibitable idiotype that does not carry the internal image of the linear primary gp41 (662)ELDKWAS(668) epitope.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Antibodies, Anti-Idiotypic / chemistry*
  • Antibodies, Anti-Idiotypic / genetics
  • Antibodies, Anti-Idiotypic / immunology
  • Antibodies, Monoclonal / chemistry*
  • Antibodies, Monoclonal / genetics
  • Antibodies, Monoclonal / immunology
  • Binding Sites
  • Crystallography, X-Ray
  • Epitopes / chemistry
  • Epitopes / genetics
  • HIV Antibodies / chemistry*
  • HIV Antibodies / genetics
  • HIV Antibodies / immunology
  • HIV Envelope Protein gp41 / chemistry
  • HIV Envelope Protein gp41 / genetics
  • HIV Envelope Protein gp41 / immunology
  • HIV-1 / immunology*
  • Humans
  • Immunoglobulin Fab Fragments / chemistry*
  • Immunoglobulin Fab Fragments / genetics
  • Immunoglobulin Fab Fragments / immunology
  • Mice
  • Models, Molecular
  • Molecular Sequence Data
  • Neutralization Tests

Substances

  • Antibodies, Anti-Idiotypic
  • Antibodies, Monoclonal
  • Epitopes
  • HIV Antibodies
  • HIV Envelope Protein gp41
  • Immunoglobulin Fab Fragments

Associated data

  • PDB/3BQU