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 21EI | pdb_000021ei

Structural and Functional Insights into VEGFR-3-Mediated Lymphangiogenesis : Unraveling the clustering mechanism of VEGFR-3/VEGF-C


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 21EI

This is version 1.0 of the entry. See complete history. 

Literature

Structural Basis of Lymphangiogenic Receptor VEGFR-3 Activation Mediated by Distinctive Clustering of the Ligand-Receptor Complex.

Cho, R., Ahn, J., Yang, J., Lee, D.S., Hong, G., Lee, S., Kim, H.M.

(2026) Adv Sci (Weinh) : e77728-e77728

  • DOI: https://doi.org/10.1002/advs.77728
  • Primary Citation Related Structures: 
    21EI, 21ES

  • PubMed Abstract: 

    Vascular endothelial growth factor-C (VEGF-C) and its receptor VEGFR-3 are critical for lymphangiogenesis, yet the structural mechanisms beyond simple dimerization that drive activation remain unknown. Here, we report the first cryo-EM structure of the human VEGFR-3 full ectodomain in complex with VEGF-C. Such a canonical ligand-induced 2:2 hetero-tetrameric complex further self-assembles into distinct higher-order assemblies-a lateral cis-cluster and an inverted trans-like-cluster. Further analysis of these canonical 2:2 hetero-tetramer in higher-order assemblies identifies that the specificity of VEGF-C for VEGFR-3 and VEGFR-2 over VEGFR-1 is mainly governed by its N-terminal α1 helix, which is structurally accommodated by the D2 domains of VEGFR-3 and VEGFR-2 but sterically excluded by the protruding D1-D2 connecting loop of VEGFR-1. Furthermore, we identify a unique interface within the membrane-proximal D5 domain occurring between neighboring canonical 2:2 complexes, mediated by a specific "WTP motif," as a key driver of cis-clustering. Structure-guided mutagenesis and real-time optogenetic assays support a critical role for cis-clustering in signal amplification and show that enforced receptor clustering can drive robust activation, whereas trans-like-clustering appears dispensable. Collectively, these findings transform the traditional "monomer-to-dimer" activation model of VEGFR-3/VEGF-C into a "dimer-to-cluster" paradigm, providing a blueprint for engineering next-generation therapeutics targeting lymphatic vascular diseases.


  • Organizational Affiliation: 
    • InnoCORE AI-CRED Institute, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 317.76 kDa 
  • Atom Count: 11,865 
  • Modeled Residue Count: 1,500 
  • Deposited Residue Count: 2,834 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor receptor 3A,
B,
C [auth E]
778Homo sapiensMutation(s): 0 
Gene Names: FLT4, VEGFR3
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P35916 (Homo sapiens)
Explore P35916 
Go to UniProtKB:  P35916
PHAROS:  P35916
GTEx:  ENSG00000037280 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35916
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Vascular endothelial growth factor CD,
E [auth C],
F [auth H],
G
125Homo sapiensMutation(s): 1 
Gene Names: VEGFC
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49767
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: 3D ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2024-00397681
National Research Foundation (NRF, Korea)Korea, Republic OfRS-2025-00523575

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-30
    Type: Initial release