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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 / Wnt receptor activity / non-canonical Wnt signaling pathway / TGFBR3 regulates TGF-beta signaling / Activation of SMO / Wnt-protein binding / apicolateral plasma membrane / negative regulation of interleukin-8 production ...midbrain morphogenesis / Signaling by RNF43 mutants / angiotensin receptor binding / Wnt receptor activity / non-canonical Wnt signaling pathway / TGFBR3 regulates TGF-beta signaling / Activation of SMO / Wnt-protein binding / apicolateral plasma membrane / negative regulation of interleukin-8 production / desensitization of G protein-coupled receptor signaling pathway / PCP/CE pathway / arrestin family protein binding / Class B/2 (Secretin family receptors) / G protein-coupled receptor internalization / stress fiber assembly / Wnt signaling pathway, planar cell polarity pathway / negative regulation of Notch signaling pathway / sensory perception / positive regulation of cardiac muscle hypertrophy / negative regulation of interleukin-6 production / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / canonical Wnt signaling pathway / pseudopodium / positive regulation of receptor internalization / insulin-like growth factor receptor binding / negative regulation of protein ubiquitination / clathrin-coated pit / intracellular glucose homeostasis / cytoplasmic vesicle membrane / Regulation of FZD by ubiquitination / enzyme inhibitor activity / negative regulation of canonical NF-kappaB signal transduction / Activated NOTCH1 Transmits Signal to the Nucleus / GTPase activator activity / negative regulation of canonical Wnt signaling pathway / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein phosphorylation / G protein-coupled receptor binding / G protein-coupled receptor activity / 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 / Signaling by BRAF and RAF1 fusions / endocytic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / protein transport / Clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / cytoplasmic vesicle / Ca2+ pathway / ubiquitin-dependent protein catabolic process / molecular adaptor activity / G alpha (s) signalling events / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / transcription coactivator 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 / DNA-templated transcription / nucleoplasm / 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 beta-arrestin engagement by the non-canonical WNT receptor FZD6 via a shallow binding pocket
Authors: Zhang, Z.B. / Lin, X. / Li, M.R. / Pan, Y.R. / Kang, Q. / Xu, F. / Zhu, X.J.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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