Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 38.76 kDa 
• Atom Count: 1876 
• Residue Count: 270 
• Unique protein chains: 2

4BSK

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

• DOI: 10.2210/pdb4BSK/pdb

• Classification: TRANSFERASE/HORMONE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2013-06-10 Released: 2013-07-31 
• Deposition Author(s): 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.

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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 

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

• PubMed: 23878260 
• 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 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3	A	214	Homo sapiens	Mutation(s): 0  Gene Names: FLT4, VEGFR3 EC: 2.7.10.1
Find proteins for P35916 (Homo sapiens) Explore P35916  Go to UniProtKB:  P35916
NIH Common Fund Data Resources
PHAROS:  P35916 GTEx:  ENSG00000037280

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
VASCULAR ENDOTHELIAL GROWTH FACTOR C	C	121	Homo sapiens	Mutation(s): 1  Gene Names: VEGFC
Find proteins for P49767 (Homo sapiens) Explore P49767  Go to UniProtKB:  P49767
NIH Common Fund Data Resources
PHAROS:  P49767 GTEx:  ENSG00000150630

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, C	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

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 = 166.66	α = 90
b = 166.66	β = 90
c = 166.66	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
autoSHARP	phasing
MOLREP	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-10 
• Released Date: 2013-07-31 
Deposition Author(s): 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.

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