3V6B

VEGFR-2/VEGF-E complex structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VEGF-E137Orf virusMutation(s): 0 
UniProt
Find proteins for P52584 (Orf virus (strain NZ2))
Explore P52584 
Go to UniProtKB:  P52584
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52584
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2B [auth R]424Homo sapiensMutation(s): 0 
Gene Names: KDRFLK1VEGFR2
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.879α = 90
b = 79.879β = 90
c = 340.044γ = 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