PDBsum entry 1bj1

Immune system

PDB id: 1bj1

Contents

Protein chains

213 a.a. *

218 a.a. *

94 a.a. *

Ligands

SO4 ×2

Waters ×548

* Residue conservation analysis

PDB id:

1bj1

Name:

Immune system

Title:

Vascular endothelial growth factor in complex with a neutralizing antibody

Structure:

Fab fragment, light chain. Chain: l, j. Synonym: fab-12. Engineered: yes. Other_details: humanized version of a monoclonal murine anti-vegf antibody. Fab fragment, heavy chain. Chain: h, k. Synonym: fab-12.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: humanized version of a monoclonal murine anti-vegf antibody. Homo sapiens. Human.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.40Å R-factor: 0.196 R-free: 0.266

Authors:

Y.A.Muller,H.W.Christinger,A.M.De Vos

Key ref:

Y.A.Muller et al. (1998). 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, 6, 1153-1167. PubMed id: 9753694 DOI: 10.1016/S0969-2126(98)00116-6

Date:

30-Jun-98 Release date: 13-Jan-99

Protein chains

No UniProt id for this chain

Struc: 213 a.a.

Protein chains

No UniProt id for this chain

Struc: 218 a.a.

Protein chains

P15692  (VEGFA_HUMAN) -  Vascular endothelial growth factor A, long form from Homo sapiens

Seq: 395 a.a.

Struc: 94 a.a.

DOI no: 10.1016/S0969-2126(98)00116-6

Structure 6:1153-1167 (1998)

PubMed id: 9753694

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.

Y.A.Muller, Y.Chen, H.W.Christinger, B.Li, B.C.Cunningham, H.B.Lowman, A.M.de Vos.

ABSTRACT

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.

Selected figure(s)

Figure 3.
Figure 3. Schematic representation of the binding epitope of VEGF for the humanized anti-VEGF antibody. Residues buried in the interface as seen in the crystal structure are colored red; residues marked with yellow display a greater than 20-fold reduction in binding affinity when changed to alanine. For comparison, and to allow discussion of the neutralizing effect of the antibody, residues buried in the interface between VEGF and domain 2 of the Flt-1 receptor [16] are colored blue, and VEGF binding determinants for KDR [15] are in green. The position of the twofold axis of the VEGF dimer is indicated by a black ellipse.

The above figure is reprinted by permission from Cell Press: Structure (1998, 6, 1153-1167) copyright 1998.

Figure was selected by an automated process.