4BSK

Crystal structure of VEGF-C in complex with VEGFR-3 domains D1-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.372 
  • R-Value Work: 0.334 
  • R-Value Observed: 0.338 

wwPDB Validation   3D Report Full Report



Literature

Structural and Mechanistic Insights Into Vegfr-3 Ligand Binding and Activation

Leppanen, V.-M.Tvorogov, D.Kisko, K.Prota, A.E.Jeltsch, M.Anisimov, A.Markovic-Mueller, S.Stuttfeld, E.Goldie, K.N.Ballmer-Hofer, K.Alitalo, K.

(2013) Proc Natl Acad Sci U S A 110: 12960

  • DOI: 10.1073/pnas.1301415110
  • Primary Citation of Related Structures:  
    4BSJ, 4BSK

  • PubMed Abstract: 
  • Vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs) are key drivers of blood and lymph vessel formation in development, but also in several pathological processes. VEGF-C signaling through VEGFR-3 promotes lymphangiogenesis, which is ...

    Vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs) are key drivers of blood and lymph vessel formation in development, but also in several pathological processes. VEGF-C signaling through VEGFR-3 promotes lymphangiogenesis, which is a clinically relevant target for treating lymphatic insufficiency and for blocking tumor angiogenesis and metastasis. The extracellular domain of VEGFRs consists of seven Ig homology domains; domains 1-3 (D1-3) are responsible for ligand binding, and the membrane-proximal domains 4-7 (D4-7) are involved in structural rearrangements essential for receptor dimerization and activation. Here we analyzed the crystal structures of VEGF-C in complex with VEGFR-3 domains D1-2 and of the VEGFR-3 D4-5 homodimer. The structures revealed a conserved ligand-binding interface in D2 and a unique mechanism for VEGFR dimerization and activation, with homotypic interactions in D5. Mutation of the conserved residues mediating the D5 interaction (Thr446 and Lys516) and the D7 interaction (Arg737) compromised VEGF-C induced VEGFR-3 activation. A thermodynamic analysis of VEGFR-3 deletion mutants showed that D3, D4-5, and D6-7 all contribute to ligand binding. A structural model of the VEGF-C/VEGFR-3 D1-7 complex derived from small-angle X-ray scattering data is consistent with the homotypic interactions in D5 and D7. Taken together, our data show that ligand-dependent homotypic interactions in D5 and D7 are essential for VEGFR activation, opening promising possibilities for the design of VEGFR-specific drugs.


    Organizational Affiliation

    Translational Cancer Biology Program, Institute for Molecular Medicine Finland and Helsinki University Central Hospital, Biomedicum Helsinki, University of Helsinki, 00014 Helsinki, Finland.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3 A214Homo sapiensMutation(s): 0 
Gene Names: FLT4VEGFR3
EC: 2.7.10.1
Find proteins for P35916 (Homo sapiens)
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Go to UniProtKB:  P35916
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PHAROS:  P35916
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
VASCULAR ENDOTHELIAL GROWTH FACTOR C C121Homo sapiensMutation(s): 1 
Gene Names: VEGFC
Find proteins for P49767 (Homo sapiens)
Explore P49767 
Go to UniProtKB:  P49767
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PHAROS:  P49767
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A, C
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • R-Value Free: 0.372 
  • R-Value Work: 0.334 
  • R-Value Observed: 0.338 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.66α = 90
b = 166.66β = 90
c = 166.66γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
autoSHARPphasing
MOLREPphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-31
    Type: Initial release
  • Version 1.1: 2013-08-21
    Changes: Database references
  • Version 1.2: 2013-08-28
    Changes: Derived calculations
  • Version 2.0: 2018-04-11
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2019-04-24
    Changes: Data collection, Source and taxonomy
  • Version 2.2: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary