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- PDB-25gn: receptor-arrestin -

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Basic information

Entry
Database: PDB / ID: 25gn
Titlereceptor-arrestin
Components
  • Frizzled-6
  • Isoform 1B of Beta-arrestin-1
  • heavy chain of scFv30
  • light chain of scFv30
KeywordsMEMBRANE PROTEIN / Receptor / Complex
Function / homology
Function and homology information


midbrain morphogenesis / Signaling by RNF43 mutants / angiotensin receptor binding / negative regulation of protein localization to ciliary membrane / Wnt receptor activity / non-canonical Wnt signaling pathway / TGFBR3 regulates TGF-beta signaling / Activation of SMO / Wnt-protein binding / protein localization to non-motile cilium ...midbrain morphogenesis / Signaling by RNF43 mutants / angiotensin receptor binding / negative regulation of protein localization to ciliary membrane / Wnt receptor activity / non-canonical Wnt signaling pathway / TGFBR3 regulates TGF-beta signaling / Activation of SMO / Wnt-protein binding / protein localization to non-motile cilium / apicolateral plasma membrane / intraciliary retrograde transport / negative regulation of interleukin-8 production / desensitization of G protein-coupled receptor signaling pathway / PCP/CE pathway / Class B/2 (Secretin family receptors) / arrestin family protein binding / G protein-coupled receptor internalization / stress fiber assembly / Wnt signaling pathway, planar cell polarity pathway / mitogen-activated protein kinase kinase binding / negative regulation of Notch signaling pathway / sensory perception / Lysosome Vesicle Biogenesis / negative regulation of interleukin-6 production / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / canonical Wnt signaling pathway / pseudopodium / positive regulation of smoothened signaling pathway / positive regulation of receptor internalization / cysteine-type endopeptidase inhibitor activity / insulin-like growth factor receptor binding / clathrin-coated pit / negative regulation of protein ubiquitination / GTPase activator activity / intracellular glucose homeostasis / Regulation of FZD by ubiquitination / enzyme inhibitor activity / negative regulation of canonical NF-kappaB signal transduction / Activated NOTCH1 Transmits Signal to the Nucleus / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of canonical Wnt signaling pathway / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cytoplasmic vesicle membrane / positive regulation of protein phosphorylation / G protein-coupled receptor binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / cilium / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / Ca2+ pathway / G alpha (s) signalling events / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / regulation of apoptotic process / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / transcription coactivator activity / protein-macromolecule adaptor activity / apical plasma membrane / protein ubiquitination / Ub-specific processing proteases / Golgi membrane / lysosomal membrane / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / endoplasmic reticulum membrane / chromatin / negative regulation of transcription by RNA polymerase II / cell surface / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Frizzled-6 / Frizzled 6, cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain ...Frizzled-6 / Frizzled 6, cysteine-rich domain / Frizzled/Smoothened, transmembrane domain / Frizzled/Smoothened family membrane region / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Immunoglobulin E-set
Similarity search - Domain/homology
Frizzled-6 / Beta-arrestin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFei, X. / Zhibin, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Pharmacol Sin / Year: 2026
Title: Direct β-arrestin engagement by the non-canonical WNT receptor FZD6 via a shallow binding pocket.
Authors: Zhi-Bin Zhang / Xi Lin / Meng-Rao Li / Yu-Rui Pan / Qing Kang / Fei Xu / Xiang-Jia Zhu /
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- ...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.
History
DepositionApr 2, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2026Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.1Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Isoform 1B of Beta-arrestin-1
H: heavy chain of scFv30
L: light chain of scFv30
R: Frizzled-6


Theoretical massNumber of molelcules
Total (without water)131,8334
Polymers131,8334
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Isoform 1B of Beta-arrestin-1 / Arrestin beta-1 / Non-visual arrestin-2


Mass: 46398.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARRB1, ARR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P49407
#2: Antibody heavy chain of scFv30


Mass: 13294.725 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Antibody light chain of scFv30


Mass: 11717.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#4: Protein Frizzled-6 / Fz-6 / hFz6


Mass: 60422.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O60353
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: FZD6 beta-arrestin 1 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.5
SpecimenConc.: 7.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71056 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037021
ELECTRON MICROSCOPYf_angle_d0.6529582
ELECTRON MICROSCOPYf_dihedral_angle_d7.061987
ELECTRON MICROSCOPYf_chiral_restr0.0471118
ELECTRON MICROSCOPYf_plane_restr0.0061182

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