4CKV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.055 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1
X
94Homo sapiensMutation(s): 0 
Gene Names: FLT1 (FLT, FRT, VEGFR1)
EC: 2.7.10.1
Find proteins for P17948 (Homo sapiens)
Go to Gene View: FLT1
Go to UniProtKB:  P17948
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
X
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
X
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.055 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.163 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 95.730α = 90.00
b = 102.390β = 90.00
c = 27.470γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2017-02-01
    Type: Database references