5T89

Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.285 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the Full-length VEGFR-1 Extracellular Domain in Complex with VEGF-A.

Markovic-Mueller, S.Stuttfeld, E.Asthana, M.Weinert, T.Bliven, S.Goldie, K.N.Kisko, K.Capitani, G.Ballmer-Hofer, K.

(2017) Structure 25: 341-352

  • DOI: 10.1016/j.str.2016.12.012

  • PubMed Abstract: 
  • Vascular endothelial growth factors (VEGFs) regulate blood and lymph vessel development upon activation of three receptor tyrosine kinases: VEGFR-1, -2, and -3. Partial structures of VEGFR/VEGF complexes based on single-particle electron microscopy, ...

    Vascular endothelial growth factors (VEGFs) regulate blood and lymph vessel development upon activation of three receptor tyrosine kinases: VEGFR-1, -2, and -3. Partial structures of VEGFR/VEGF complexes based on single-particle electron microscopy, small-angle X-ray scattering, and X-ray crystallography revealed the location of VEGF binding and domain arrangement of individual receptor subdomains. Here, we describe the structure of the full-length VEGFR-1 extracellular domain in complex with VEGF-A at 4 Å resolution. We combined X-ray crystallography, single-particle electron microscopy, and molecular modeling for structure determination and validation. The structure reveals the molecular details of ligand-induced receptor dimerization, in particular of homotypic receptor interactions in immunoglobulin homology domains 4, 5, and 7. Functional analyses of ligand binding and receptor activation confirm the relevance of these homotypic contacts and identify them as potential therapeutic sites to allosterically inhibit VEGFR-1 activity.


    Organizational Affiliation

    Paul Scherrer Institute, Laboratory of Biomolecular Research, 5232 Villigen, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor A
V, W
131Homo sapiensMutation(s): 0 
Gene Names: VEGFA (VEGF)
Find proteins for P15692 (Homo sapiens)
Go to Gene View: VEGFA
Go to UniProtKB:  P15692
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Vascular endothelial growth factor receptor 1
X, Y
646Homo 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
V, W, X, Y
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.285 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 166.710α = 90.00
b = 123.090β = 109.56
c = 167.370γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland31003A-130463
OncosuisseSwitzerlandOC2 01200-08-2007

Revision History 

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-02-15
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Advisory, Author supporting evidence, Data collection
  • Version 1.3: 2017-10-11
    Type: Data collection