2XAC

Structural Insights into the Binding of VEGF-B by VEGFR-1D2: Recognition and Specificity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.364 
  • R-Value Work: 0.282 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Insights Into the Binding of Vegf-B by Vegfr-1D2: Recognition and Specificity

Iyer, S.Darley, P.Acharya, K.R.

(2010) J.Biol.Chem. 285: 23779

  • DOI: 10.1074/jbc.M110.130658

  • PubMed Abstract: 
  • The formation of blood vessels (angiogenesis) is a highly orchestrated sequence of events involving crucial receptor-ligand interactions. Angiogenesis is critical for physiological processes such as development, wound healing, reproduction, tissue re ...

    The formation of blood vessels (angiogenesis) is a highly orchestrated sequence of events involving crucial receptor-ligand interactions. Angiogenesis is critical for physiological processes such as development, wound healing, reproduction, tissue regeneration, and remodeling. It also plays a major role in sustaining tumor progression and chronic inflammation. Vascular endothelial growth factor (VEGF)-B, a member of the VEGF family of angiogenic growth factors, effects blood vessel formation by binding to a tyrosine kinase receptor, VEGFR-1. There is growing evidence of the important role played by VEGF-B in physiological and pathological vasculogenesis. Development of VEGF-B antagonists, which inhibit the interaction of this molecule with its cognate receptor, would be important for the treatment of pathologies associated specifically with this growth factor. In this study, we present the crystal structure of the complex of VEGF-B with domain 2 of VEGFR-1 at 2.7 A resolution. Our analysis reveals that each molecule of the ligand engages two receptor molecules using two symmetrical binding sites. Based on these interactions, we identify the receptor-binding determinants on VEGF-B and shed light on the differences in specificity towards VEGFR-1 among the different VEGF homologs.


    Organizational Affiliation

    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VASCULAR ENDOTHELIAL GROWTH FACTOR B
A, B
99Homo sapiensMutation(s): 0 
Gene Names: VEGFB (VRF)
Find proteins for P49765 (Homo sapiens)
Go to Gene View: VEGFB
Go to UniProtKB:  P49765
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
C, X
98Homo sapiensMutation(s): 0 
Gene Names: FLT1 (FLT, FRT, VEGFR1)
EC: 2.7.10.1
Find proteins for P17948 (Homo sapiens)
Go to Gene View: FLT1
Go to UniProtKB:  P17948
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.364 
  • R-Value Work: 0.282 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.212α = 90.00
b = 65.526β = 90.26
c = 82.824γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance