4CKV | pdb_00004ckv

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

• PDB DOI: https://doi.org/10.2210/pdb4CKV/pdb

• Classification: RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-01-09 Released: 2015-01-28 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.205 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

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

• PubMed: 27942001 
• DOI: https://doi.org/10.1371/journal.pone.0167755
• Primary Citation 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.

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Organizational Affiliation: 
• UMR 8015 CNRS - Université Paris Descartes, Faculté de Pharmacie, Sorbonne Paris Cité, Paris, France.
UMR 8638 CNRS - Université Paris Descartes, Faculté de Pharmacie, Sorbonne Paris Cité, Paris, France.
Centre de Recherche Insulaire et Observatoire de l'Environnement USR CNRS 3278 CRIOBE, Université de Perpignan Via Domitia, Perpignan, France.
UF Pharmacocinétique et Pharmacochimie, hôpital Cochin, AP-HP, Paris, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 11.12 kDa 
• Atom Count: 897 
• Modeled Residue Count: 94 
• Deposited Residue Count: 94 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1	A [auth X]	94	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth X]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	C [auth X], D [auth X], E [auth X], F [auth X]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.205 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.73	α = 90
b = 102.39	β = 90
c = 27.47	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-28 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2015-01-28
  Type: Initial release
  
• Version 1.1: 2017-02-01
  Changes: Database references
• Version 2.0: 2019-03-06
  Changes: Atomic model, Data collection, Experimental preparation, Other
• Version 2.1: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 2.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 2.3: 2024-11-20
  Changes: Structure summary