8XFS | pdb_00008xfs

LGR4-RSPO2-ZNRF3 RING domain (1:2:2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the LGR4-RSPO2-ZNRF3 complexes regulating WNT/ beta-catenin signaling.

Wang, L.Hu, F.Cui, Q.Qiao, H.Li, L.Geng, T.Li, Y.Sun, Z.Zhou, S.Lan, Z.Guo, S.Hu, Y.Wang, J.Yang, Q.Wang, Z.Dai, Y.Geng, Y.

(2025) Nat Commun 16: 362-362

  • DOI: https://doi.org/10.1038/s41467-024-55431-3
  • Primary Citation of Related Structures:  
    8XFP, 8XFS, 8XFT, 8Y69

  • PubMed Abstract: 

    WNT/β-catenin signaling plays key roles in development and cancer 1,2 . ZNRF3/RNF43 modulates Frizzleds through ubiquitination, dampening WNT/β-catenin signaling. Conversely, RSPO1-4 binding to LGR4-6 and ZNRF3/RNF43 enhances WNT/β-catenin signaling 3-5 . Here, we elucidate the overall landscape of architectures in multiple LGR4, RSPO2, and ZNRF3 assemblies, showcasing varying stoichiometries and arrangements. These structures reveal that LGR4 and RSPO2 capture distinct states of ZNRF3. The intrinsic heterogeneity of the LGR4-RSPO2-ZNRF3 assembly is influenced by LGR4 content. Particularly, in the assembly complex with a 2:2:2 ratio, two LGR4 protomers induce and stabilize the inactive state of ZNRF3, characterized by a wide inward-open conformation of two transmembrane helices (TM helices). This specific assembly promotes a stable complex, facilitating LGR4-induced endocytosis of ZNRF3. In contrast, the active dimeric ZNRF3, bound by a single LGR4, adopts a coiled-coil TM helices conformation and dimerization of RING domains. Our findings unveil how LGR4 content mediates diverse assemblies, leading to conformational rearrangements in ZNRF3 to regulate WNT/β-catenin signaling, and provide a structural foundation for drug development targeting Wnt-driven cancers.


  • Organizational Affiliation
    • State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat-containing G-protein coupled receptor 4791Homo sapiensMutation(s): 0 
Gene Names: LGR4GPR48
Membrane Entity: Yes 
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
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase ZNRF3B [auth C],
E
190Homo sapiensMutation(s): 0 
Gene Names: ZNRF3KIAA1133RNF203
EC: 2.3.2.27
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULT6 (Homo sapiens)
Explore Q9ULT6 
Go to UniProtKB:  Q9ULT6
PHAROS:  Q9ULT6
GTEx:  ENSG00000183579 
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UniProt GroupQ9ULT6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody Nb52C [auth F]106Camelus bactrianusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
R-spondin-2D [auth B],
F [auth D]
101Homo sapiensMutation(s): 0 
Gene Names: Rspo2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q6UXX9 (Homo sapiens)
Explore Q6UXX9 
Go to UniProtKB:  Q6UXX9
PHAROS:  Q6UXX9
GTEx:  ENSG00000147655 
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UniProt GroupQ6UXX9
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedChina--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Data collection, Database references