8ZXD | pdb_00008zxd

the Planar Cell Polarity Core Protein Vangl1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure and oligomerization of the human planar cell polarity core protein Vangl1.

Zhang, F.Li, S.Wu, H.Chen, S.

(2025) Nat Commun 16: 135-135

  • DOI: https://doi.org/10.1038/s41467-024-55397-2
  • Primary Citation of Related Structures:  
    8ZXD

  • PubMed Abstract: 

    Vangl is a planar cell polarity (PCP) core protein essential for aligned cell orientation along the epithelial plane perpendicular to the apical-basal direction, which is important for tissue morphogenesis, development and collective cell behavior. Mutations in Vangl are associated with developmental defects, including neural tube defects (NTDs), according to human cohort studies of sporadic and familial cases. The complex mechanisms underlying Vangl-mediated PCP signaling or Vangl-associated human congenital diseases have been hampered by the lack of molecular characterizations of Vangl. Here, we show biochemical and structural evidence that human Vangl1 oligomerizes as dimers of trimers, and that the dimerization of trimers promotes binding to the PCP effector Prickle1 (Pk1) in vitro. Mapping of human disease-associated point mutations suggests potential pathological mechanisms and paves the way for future studies on the importance of lipid binding, central vestibule and oligomerization of Vangl, thereby providing insights into the molecular mechanisms of the PCP signaling pathway.


  • Organizational Affiliation
    • Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vang-like protein 1
A, B, C, D, E
A, B, C, D, E, F
524Homo sapiensMutation(s): 0 
Gene Names: VANGL1STB2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAA9 (Homo sapiens)
Explore Q8TAA9 
Go to UniProtKB:  Q8TAA9
PHAROS:  Q8TAA9
GTEx:  ENSG00000173218 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TAA9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MC3 (Subject of Investigation/LOI)
Query on MC3

Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
O [auth C]
Q [auth D]
T [auth E]
H [auth A],
K [auth B],
O [auth C],
Q [auth D],
T [auth E],
X [auth F]
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE
C36 H72 N O8 P
CITHEXJVPOWHKC-UUWRZZSWSA-N
Y01 (Subject of Investigation/LOI)
Query on Y01

Download Ideal Coordinates CCD File 
G [auth A]
I [auth A]
J [auth B]
L [auth B]
M [auth C]
G [auth A],
I [auth A],
J [auth B],
L [auth B],
M [auth C],
N [auth C],
P [auth D],
R [auth D],
S [auth E],
U [auth E],
V [auth F],
W [auth F]
CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82101213

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-23
    Changes: Data collection