25GN | pdb_000025gn

receptor-arrestin


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 25GN

This is version 1.1 of the entry. See complete history

Literature

Direct beta-arrestin engagement by the non-canonical WNT receptor FZD6 via a shallow binding pocket.

Zhang, Z.B.Lin, X.Li, M.R.Pan, Y.R.Kang, Q.Xu, F.Zhu, X.J.

(2026) Acta Pharmacol Sin 

  • DOI: https://doi.org/10.1038/s41401-026-01902-w
  • Primary Citation Related Structures: 
    25GN

  • PubMed Abstract: 

    As primary WNT receptors, Frizzled (FZD) receptors behave as nonclassical GPCRs; however, their engagement with downstream transducers is largely unknown. Previous studies have suggested that β-arrestin recruitment to FZD receptors depends on its interaction with Dishevelled (DVL) and that this process regulates both canonical and non-canonical pathways. Here, we reveal that FZD6, which mainly mediates non-canonical WNT signalling, directly binds to β-arrestin 1 (βarr1) and report the cryo-EM structure of the FZD6-βarr1 complex, which revealed a unique shallow pocket in FZD6 for βarr1 engagement and identified arrestin-specific motifs that are distinct from those observed in previously reported FZD receptor-transducer complexes. Collectively, our findings establish a direct arrestin recruitment mechanism in FZD receptors that shares key features with arrestin engagement in classical GPCRs, suggesting that the engagement of core GPCR transducers may modulate WNT signalling specificity. These insights position FZD receptors as druggable targets akin to classical GPCRs, opening new avenues for targeting FZD receptors for a wide range of diseases, including cancer.


  • Organizational Affiliation
    • Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.

Macromolecule Content 

  • Total Structure Weight: 131.83 kDa 
  • Atom Count: 6,853 
  • Modeled Residue Count: 902 
  • Deposited Residue Count: 1,163 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 1B of Beta-arrestin-1A [auth C]410Homo sapiensMutation(s): 0 
Gene Names: ARRB1ARR1
UniProt & NIH Common Fund Data Resources
Find proteins for P49407 (Homo sapiens)
Explore P49407 
Go to UniProtKB:  P49407
PHAROS:  P49407
GTEx:  ENSG00000137486 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49407
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
heavy chain of scFv30B [auth H]121Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
light chain of scFv30C [auth L]108Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Frizzled-6D [auth R]524Homo sapiensMutation(s): 0 
Gene Names: FZD6
UniProt & NIH Common Fund Data Resources
Find proteins for O60353 (Homo sapiens)
Explore O60353 
Go to UniProtKB:  O60353
PHAROS:  O60353
GTEx:  ENSG00000164930 
Entity Groups
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UniProt GroupO60353
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Reference Sequence

Small Molecules

Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
D [auth R]L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
D [auth R]L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • 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
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-26
    Type: Initial release
  • Version 1.1: 2026-09-02
    Changes: Data collection, Database references