Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 102.11 kDa 
• Atom Count: 2114 
• Residue Count: 280 
• Unique protein chains: 2

3V2A

VEGFR-2/VEGF-A COMPLEX STRUCTURE

• DOI: 10.2210/pdb3V2A/pdb

• Classification: HORMONE/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda, Komagataella pastoris
• Mutation(s): No 


• Deposited: 2011-12-12 Released: 2012-01-18 
• Deposition Author(s): Brozzo, M.S., Leppanen, V.-M., Winkler, F.K., Ballmer-Hofer, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.300 
• R-Value Work: 0.244 
• R-Value Observed: 0.247 

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

• PubMed: 22207738 
• DOI: 10.1182/blood-2011-11-390922
• Primary Citation of Related Structures:  
  3V6B, 3V2A


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor receptor 2	R	772	Homo sapiens	Mutation(s): 0  Gene Names: FLK1, KDR, VEGFR2 EC: 2.7.10.1
Find proteins for P35968 (Homo sapiens) Explore P35968  Go to UniProtKB:  P35968
NIH Common Fund Data Resources
PHAROS:  P35968 GTEx:  ENSG00000128052

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Vascular endothelial growth factor A	A	134	Homo sapiens	Mutation(s): 0  Gene Names: VEGF, VEGF-A, VEGFA
Find proteins for P15692 (Homo sapiens) Explore P15692  Go to UniProtKB:  P15692
NIH Common Fund Data Resources
PHAROS:  P15692 GTEx:  ENSG00000112715

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.300 
• R-Value Work: 0.244 
• R-Value Observed: 0.247 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.969	α = 90
b = 80.969	β = 90
c = 332.063	γ = 120

Software Package:

Software Name	Purpose
RemDAq	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-12-12 
• Released Date: 2012-01-18 
Deposition Author(s): Brozzo, M.S., Leppanen, V.-M., Winkler, F.K., Ballmer-Hofer, K.

Revision History 

• 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