4CL7

Crystal structure of VEGFR-1 domain 2 in presence of Cobalt


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Biophysical Studies of the Induced Dimerization of Human Vegf R Receptor 1 Binding Domain by Divalent Metals Competing with Vegf-A

Gaucher, J.-F.Reille-Seroussi, M.Gagey-Eilstein, N.Broussy, S.Coric, P.Seijo, B.Lascombe, M.-B.Gautier, B.Liu, W.-Q.Huguenot, F.Inguimbert, N.Bouaziz, S.Vidal, M.Broutin, I.

(2016) PLoS One 11: 67755

  • DOI: 10.1371/journal.pone.0167755
  • Primary Citation of Related Structures:  
    5ABD, 4CKV, 4CL7

  • PubMed Abstract: 
  • Angiogenesis is tightly regulated through the binding of vascular endothelial growth factors (VEGFs) to their receptors (VEGFRs). In this context, we showed that human VEGFR1 domain 2 crystallizes in the presence of Zn2+, Co2+ or Cu2+ as a dimer that forms via metal-ion interactions and interlocked hydrophobic surfaces ...

    Angiogenesis is tightly regulated through the binding of vascular endothelial growth factors (VEGFs) to their receptors (VEGFRs). In this context, we showed that human VEGFR1 domain 2 crystallizes in the presence of Zn2+, Co2+ or Cu2+ as a dimer that forms via metal-ion interactions and interlocked hydrophobic surfaces. SAXS, NMR and size exclusion chromatography analyses confirm the formation of this dimer in solution in the presence of Co2+, Cd2+ or Cu2+. Since the metal-induced dimerization masks the VEGFs binding surface, we investigated the ability of metal ions to displace the VEGF-A binding to hVEGFR1: using a competition assay, we evidenced that the metals displaced the VEGF-A binding to hVEGFR1 extracellular domain binding at micromolar level.


    Organizational Affiliation

    UMR 8015 CNRS - Université Paris Descartes, Faculté de Pharmacie, Sorbonne Paris Cité, Paris, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1A, B, C, D94Homo sapiensMutation(s): 0 
Gene Names: FLT1FLTFRTVEGFR1
EC: 2.7.10.1
Find proteins for P17948 (Homo sapiens)
Explore P17948 
Go to UniProtKB:  P17948
NIH Common Fund Data Resources
PHAROS:  P17948
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.171 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 27.746α = 87.05
b = 41.711β = 82.25
c = 94.694γ = 73.03
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other