10RK | pdb_000010rk

Heparin-induced trans tetrameric complex of VEGF, VEGFR2 and Neuropilin 1

  • Classification: SIGNALING PROTEIN
  • Organism(s): Mus musculus
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2026-02-03 Released: 2026-06-10 
  • Deposition Author(s): Chen, L., Bai, X., Zhang, X.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Robert A. Welch Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 10RK

This is version 1.1 of the entry. See complete history

Literature

Mechanisms of VEGFR2 activation by VEGF, neuropilin, and heparin.

Chen, L.Sun, Z.Qiao, J.Bai, X.C.Zhang, X.

(2026) Sci Adv 12: eaeg6323-eaeg6323

  • DOI: https://doi.org/10.1126/sciadv.aeg6323
  • Primary Citation Related Structures: 
    10RI, 10RJ, 10RK

  • PubMed Abstract: 

    Vascular endothelial growth factor (VEGF) and its receptor VEGFR are master regulators of vasculogenesis and angiogenesis. VEGF activates VEGFR by inducing its dimerization and trans-autophosphorylation. The coreceptor neuropilin (Nrp1 and Nrp2) and heparan sulfate proteoglycan (HSPG) modulate VEGF-VEGFR signaling, but the underlying mechanisms remain incompletely understood. Here we report a cryo-EM structure of the dimeric mouse VEGF 164 -VEGFR2-Nrp1 ectodomain complex with a 2:2:2 stoichiometry, revealing direct Nrp1-VEGFR2 interactions that stabilize the VEGFR2 dimer. We also determined two cryo-EM structures of the VEGF 164 -VEGFR2-Nrp1 complex in the presence of short- or long-chain heparin, which bridges all three proteins and promotes the formation of two distinct tetrameric complexes. Long-chain heparin induces a cis tetrameric complex consistent with receptor clustering on the same cell surface, whereas short-chain heparin promotes a trans tetrameric assembly which might be formed by two dimeric complexes from opposing cells. Our structure-based mutational analyses support the model that both the Nrp1-VEGFR2 interface and the heparin-mediated clustering enhance VEGFR2 signaling.


  • Organizational Affiliation
    • Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.

Macromolecule Content 

  • Total Structure Weight: 809.72 kDa 
  • Atom Count: 41,466 
  • Modeled Residue Count: 5,196 
  • Deposited Residue Count: 7,104 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neuropilin-1A [auth E],
B [auth K],
F,
K [auth L]
847Mus musculusMutation(s): 0 
Gene Names: Nrp1Nrp
UniProt & NIH Common Fund Data Resources
Find proteins for P97333 (Mus musculus)
Explore P97333 
Go to UniProtKB:  P97333
IMPC:  MGI:106206
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97333
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P97333-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform VEGF-1 of Vascular endothelial growth factor A, long formC [auth A],
D [auth B],
H [auth G],
I [auth H]
175Mus musculusMutation(s): 0 
Gene Names: VegfaVegf
UniProt
Find proteins for Q00731 (Mus musculus)
Explore Q00731 
Go to UniProtKB:  Q00731
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00731
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 2E [auth C],
G [auth D],
J [auth I],
L [auth J]
754Mus musculusMutation(s): 0 
Gene Names: KdrFlk-1Flk1
EC: 2.7.10.1
UniProt
Find proteins for P35918 (Mus musculus)
Explore P35918 
Go to UniProtKB:  P35918
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35918
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P35918-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
M, N
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose
O, P
6N/A
Glycosylation Resources
GlyTouCan: G30141AL
GlyCosmos: G30141AL

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
BA [auth D]
CA [auth D]
DA [auth I]
EA [auth I]
FA [auth L]
BA [auth D],
CA [auth D],
DA [auth I],
EA [auth I],
FA [auth L],
IA [auth J],
JA [auth J],
Q [auth E],
T [auth K],
W [auth C],
X [auth C],
Y [auth F]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
AA [auth F]
GA [auth L]
HA [auth L]
R [auth E]
S [auth E]
AA [auth F],
GA [auth L],
HA [auth L],
R [auth E],
S [auth E],
U [auth K],
V [auth K],
Z [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_4924
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM130289
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM156386
Robert A. Welch FoundationUnited StatesI-1702
Robert A. Welch FoundationUnited StatesI-1944

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-10
    Type: Initial release
  • Version 1.1: 2026-07-29
    Changes: Data collection, Database references