1BJ1

VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH A NEUTRALIZING ANTIBODY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

Starting Models: experimental
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This is version 1.4 of the entry. See complete history


Literature

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.

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

(1998) Structure 6: 1153-1167

  • DOI: https://doi.org/10.1016/s0969-2126(98)00116-6
  • Primary Citation of Related Structures:  
    1BJ1

  • PubMed Abstract: 

    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. 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. 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.


  • Organizational Affiliation

    Department of Protein Engineering Genentech, Inc. 1 DNA Way, South San Francisco, CA 94080, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment, light chainA [auth L],
E [auth J]
214Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab fragment, heavy chainB [auth H],
F [auth K]
231Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor AC [auth V],
D [auth W]
102Homo sapiensMutation(s): 0 
Gene Names: VEGFAVEGF
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens)
Explore P15692 
Go to UniProtKB:  P15692
PHAROS:  P15692
GTEx:  ENSG00000112715 
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UniProt GroupP15692
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.86α = 90
b = 66.98β = 94.27
c = 140.51γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-09-26
    Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.4: 2023-08-02
    Changes: Database references, Derived calculations, Refinement description