2X1X

CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF VEGFR2 IN A TETRAGONAL CRYSTAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Determinants of Growth Factor Binding and Specificity by Vegf Receptor 2.

Leppanen, V.-M.Prota, A.E.Jeltsch, M.Anisimov, A.Kalkkinen, N.Strandin, T.Lankinen, H.Goldman, A.Ballmer-Hofer, K.Alitalo, K.

(2010) Proc.Natl.Acad.Sci.USA 107: 2425

  • DOI: 10.1073/pnas.0914318107
  • Primary Citation of Related Structures:  2X1W

  • PubMed Abstract: 
  • Vascular endothelial growth factors (VEGFs) regulate blood and lymph vessel formation through activation of three receptor tyrosine kinases, VEGFR-1, -2, and -3. The extracellular domain of VEGF receptors consists of seven immunoglobulin homology dom ...

    Vascular endothelial growth factors (VEGFs) regulate blood and lymph vessel formation through activation of three receptor tyrosine kinases, VEGFR-1, -2, and -3. The extracellular domain of VEGF receptors consists of seven immunoglobulin homology domains, which, upon ligand binding, promote receptor dimerization. Dimerization initiates transmembrane signaling, which activates the intracellular tyrosine kinase domain of the receptor. VEGF-C stimulates lymphangiogenesis and contributes to pathological angiogenesis via VEGFR-3. However, proteolytically processed VEGF-C also stimulates VEGFR-2, the predominant transducer of signals required for physiological and pathological angiogenesis. Here we present the crystal structure of VEGF-C bound to the VEGFR-2 high-affinity-binding site, which consists of immunoglobulin homology domains D2 and D3. This structure reveals a symmetrical 22 complex, in which left-handed twisted receptor domains wrap around the 2-fold axis of VEGF-C. In the VEGFs, receptor specificity is determined by an N-terminal alpha helix and three peptide loops. Our structure shows that two of these loops in VEGF-C bind to VEGFR-2 subdomains D2 and D3, while one interacts primarily with D3. Additionally, the N-terminal helix of VEGF-C interacts with D2, and the groove separating the two VEGF-C monomers binds to the D2/D3 linker. VEGF-C, unlike VEGF-A, does not bind VEGFR-1. We therefore created VEGFR-1/VEGFR-2 chimeric proteins to further study receptor specificity. This biochemical analysis, together with our structural data, defined VEGFR-2 residues critical for the binding of VEGF-A and VEGF-C. Our results provide significant insights into the structural features that determine the high affinity and specificity of VEGF/VEGFR interactions.


    Organizational Affiliation

    Molecular Cancer Biology Program, Biomedicum Helsinki, Department of Pathology, Haartman Institute and Helsinki University Central Hospital, PO Box 63, University of Helsinki, Haartmaninkatu 8, FI-00014 Helsinki, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VASCULAR ENDOTHELIAL GROWTH FACTOR C
E
110Homo sapiensGene Names: VEGFC
Find proteins for P49767 (Homo sapiens)
Go to Gene View: VEGFC
Go to UniProtKB:  P49767
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2
R
213Homo sapiensGene Names: KDR (FLK1, VEGFR2)
EC: 2.7.10.1
Find proteins for P35968 (Homo sapiens)
Go to Gene View: KDR
Go to UniProtKB:  P35968
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BMA
Query on BMA

Download SDF File 
Download CCD File 
E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
E, R
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
HG
Query on HG

Download SDF File 
Download CCD File 
R
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.266 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 88.733α = 90.00
b = 88.733β = 90.00
c = 105.273γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
XDSdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-08-10
    Type: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2017-07-12
    Type: Advisory, Derived calculations