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 1.3 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: https://doi.org/10.1371/journal.pone.0167755
  • Primary Citation of Related Structures:  
    4CKV, 4CL7, 5ABD

  • 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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
A, B, C, D
94Homo sapiensMutation(s): 0 
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P17948 (Homo sapiens)
Explore P17948 
Go to UniProtKB:  P17948
PHAROS:  P17948
GTEx:  ENSG00000102755 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17948
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CO
Query on CO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
J [auth B],
K [auth B],
N [auth C]
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
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 

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
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description