9KB6 | pdb_00009kb6

Cryo-EM structure of LGR4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into Wnt/ beta-catenin signaling regulation by LGR4, R-spondin, and ZNRF3.

Peng, Y.Fujimura, A.Asami, J.Zhang, Z.Shimizu, T.Ohto, U.

(2025) Nat Commun 16: 8337-8337

  • DOI: https://doi.org/10.1038/s41467-025-64129-z
  • Primary Citation of Related Structures:  
    9KB6, 9KB7, 9KB8, 9KB9

  • PubMed Abstract: 

    Leucine-rich repeat-containing G protein-coupled receptor 4 (LGR4) plays a critical role in regulating the wingless-related integration site (Wnt) signaling pathway and is essential for organ development and carcinogenesis. LGR4, along with its ligand R-spondin (RSPO), potentiates Wnt/β-catenin signaling by recruiting its signaling suppressor, E3 ligase Zinc and Ring Finger 3 (ZNRF3), and inducing its membrane clearance. However, detailed mechanisms underlying this process remain unknown. In this study, we present the cryo-electron microscopy structures of human LGR4, the LGR4-RSPO2 and LGR4-RSPO2-ZNRF3 complexes. Upon RSPO2 binding, LGR4 undergoes no significant conformational changes in its transmembrane and extracellular domain structures or their relative orientations. LGR4, RSPO2, and ZNRF3 assemble into a 2:2:2 complex with the ZNRF3 dimer enclosed at the center. This ternary arrangement and forced dimerization of ZNRF3 likely underpin how LGR4 and RSPO2 potentiate Wnt/β-catenin signaling by sequestering ZNRF3 from Wnt receptors and facilitating its auto-inactivation. This study provides a structural basis for understanding the regulatory mechanism of Wnt/β-catenin signaling through the LGR4-RSPO2-ZNRF3 pathway and may offer opportunities for future drug development targeting this axis.


  • Organizational Affiliation
    • Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat-containing G-protein coupled receptor 4845Homo sapiensMutation(s): 0 
Gene Names: LGR4GPR48
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXB1 (Homo sapiens)
Explore Q9BXB1 
Go to UniProtKB:  Q9BXB1
PHAROS:  Q9BXB1
GTEx:  ENSG00000205213 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BXB1
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q9BXB1-1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan22K15046 and 24K09349 (Z.Z.); 22H05184 and 23H00366 (T.S.); and 22H02556 (U.O.)

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release