VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 A resolution and mutational analysis of the interface

Structure. 1998 Sep 15;6(9):1153-67. doi: 10.1016/s0969-2126(98)00116-6.


Background: Vascular endothelial growth factor (VEGF) is a highly specific angiogenic growth factor; anti-angiogenic treatment through inhibition of receptor activation by VEGF might have important therapeutic applications in diseases such as diabetic retinopathy and cancer. A neutralizing anti-VEGF antibody shown to suppress tumor growth in an in vivo murine model has been used as the basis for production of a humanized version.

Results: We present the crystal structure of the complex between VEGF and the Fab fragment of this humanized antibody, as well as a comprehensive alanine-scanning analysis of the contact residues on both sides of the interface. Although the VEGF residues critical for antibody binding are distinct from those important for high-affinity receptor binding, they occupy a common region on VEGF, demonstrating that the neutralizing effect of antibody binding results from steric blocking of VEGF-receptor interactions. Of the residues buried in the VEGF-Fab interface, only a small number are critical for high-affinity binding; the essential VEGF residues interact with those of the Fab fragment, generating a remarkable functional complementarity at the interface.

Conclusions: Our findings suggest that the character of antigen-antibody interfaces is similar to that of other protein-protein interfaces, such as ligand-receptor interactions; in the case of VEGF, the principal difference is that the residues essential for binding to the Fab fragment are concentrated in one continuous segment of polypeptide chain, whereas those essential for binding to the receptor are distributed over four different segments and span across the dimer interface.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alanine / chemistry
  • Amino Acid Sequence
  • Amino Acid Substitution
  • Antibodies, Monoclonal / chemistry
  • Antibodies, Monoclonal / metabolism
  • Antigen-Antibody Complex / chemistry*
  • Antigen-Antibody Complex / genetics*
  • Antigen-Antibody Complex / immunology
  • Crystallography, X-Ray
  • DNA Mutational Analysis
  • Dimerization
  • Endothelial Growth Factors / chemistry*
  • Endothelial Growth Factors / genetics*
  • Endothelial Growth Factors / immunology
  • Epitope Mapping
  • Humans
  • Immunoglobulin Fab Fragments / chemistry*
  • Immunoglobulin Fab Fragments / genetics*
  • Immunoglobulin Fab Fragments / immunology
  • Lymphokines / chemistry*
  • Lymphokines / genetics*
  • Lymphokines / immunology
  • Models, Molecular
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Protein Binding
  • Protein Conformation
  • Protein Folding
  • Vascular Endothelial Growth Factor A
  • Vascular Endothelial Growth Factors


  • Antibodies, Monoclonal
  • Antigen-Antibody Complex
  • Endothelial Growth Factors
  • Immunoglobulin Fab Fragments
  • Lymphokines
  • Vascular Endothelial Growth Factor A
  • Vascular Endothelial Growth Factors
  • Alanine

Associated data

  • PDB/1BJ1