3V2A | pdb_00003v2a

VEGFR-2/VEGF-A COMPLEX STRUCTURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.300 (Depositor), 0.307 (DCC) 
  • R-Value Work: 
    0.244 (Depositor), 0.261 (DCC) 
  • R-Value Observed: 
    0.247 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3V2A

This is version 1.4 of the entry. See complete history

Literature

Thermodynamic and structural description of allosterically regulated VEGFR-2 dimerization.

Brozzo, M.S.Bjelic, S.Kisko, K.Schleier, T.Leppanen, V.M.Alitalo, K.Winkler, F.K.Ballmer-Hofer, K.

(2012) Blood 119: 1781-1788

  • DOI: https://doi.org/10.1182/blood-2011-11-390922
  • Primary Citation Related Structures: 
    3V2A, 3V6B

  • PubMed Abstract: 

    VEGFs activate 3 receptor tyrosine kinases, VEGFR-1, VEGFR-2, and VEGFR-3, promoting angiogenic and lymphangiogenic signaling. The extracellular receptor domain (ECD) consists of 7 Ig-homology domains; domains 2 and 3 (D23) represent the ligand-binding domain, whereas the function of D4-7 is unclear. Ligand binding promotes receptor dimerization and instigates transmembrane signaling and receptor kinase activation. In the present study, isothermal titration calorimetry showed that the Gibbs free energy of VEGF-A, VEGF-C, or VEGF-E binding to D23 or the full-length ECD of VEGFR-2 is dominated by favorable entropic contribution with enthalpic penalty. The free energy of VEGF binding to the ECD is 1.0-1.7 kcal/mol less favorable than for binding to D23. A model of the VEGF-E/VEGFR-2 ECD complex derived from small-angle scattering data provided evidence for homotypic interactions in D4-7. We also solved the crystal structures of complexes between VEGF-A or VEGF-E with D23, which revealed comparable binding surfaces and similar interactions between the ligands and the receptor, but showed variation in D23 twist angles. The energetically unfavorable homotypic interactions in D4-7 may be required for re-orientation of receptor monomers, and this mechanism might prevent ligand-independent activation of VEGFR-2 to evade the deleterious consequences for blood and lymph vessel homeostasis arising from inappropriate receptor activation.


  • Organizational Affiliation
    • Biomolecular Research, Molecular Cell Biology Paul Scherrer Institut, Villigen, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 102.11 kDa 
  • Atom Count: 2,114 
  • Modeled Residue Count: 280 
  • Deposited Residue Count: 906 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2A [auth R]772Homo sapiensMutation(s): 0 
Gene Names: FLK1KDRVEGFR2
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P35968 (Homo sapiens)
Explore P35968 
Go to UniProtKB:  P35968
PHAROS:  P35968
GTEx:  ENSG00000128052 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35968
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor AB [auth A]134Homo sapiensMutation(s): 0 
Gene Names: VEGFVEGF-AVEGFA
UniProt & NIH Common Fund Data Resources
Find proteins for P15692 (Homo sapiens)
Explore P15692 
Go to UniProtKB:  P15692
PHAROS:  P15692
GTEx:  ENSG00000112715 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15692
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.300 (Depositor), 0.307 (DCC) 
  • R-Value Work:  0.244 (Depositor), 0.261 (DCC) 
  • R-Value Observed: 0.247 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.969α = 90
b = 80.969β = 90
c = 332.063γ = 120
Software Package:
Software NamePurpose
RemDAqdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-01-18
    Type: Initial release
  • Version 1.1: 2012-03-07
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-04-03
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary