Experimental Data Snapshot
Starting Model:experimental
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(2010) Proc Natl Acad Sci U S A 107: 2425
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.
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (NAG)
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content 
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| VASCULAR ENDOTHELIAL GROWTH FACTOR C | A [auth E] | 110 | Homo sapiens | Mutation(s): 1  | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P49767 (Homo sapiens) Explore P49767  Go to UniProtKB:  P49767 | |||||
PHAROS:  P49767 GTEx:  ENSG00000150630  | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P49767 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 2 | B [auth R] | 213 | Homo sapiens | Mutation(s): 0  EC: 2.7.10.1 | ![]() |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P35968 (Homo sapiens) Explore P35968  Go to UniProtKB:  P35968 | |||||
PHAROS:  P35968 GTEx:  ENSG00000128052  | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P35968 | ||||
Glycosylation | |||||
| Glycosylation Sites: 1 | Go to GlyGen: P35968-1 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
| beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C [auth A], D [auth B] | 3 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE | |||||
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG Query on NAG Download Ideal Coordinates CCD File  | H [auth R] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
| HG Query on HG Download Ideal Coordinates CCD File  | G [auth R] | MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N | |||
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 88.733 | α = 90 |
| b = 88.733 | β = 90 |
| c = 105.273 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| MOLREP | phasing |
RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.