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4f0a

Crystal structure of XWnt8 in complex with the cysteine-rich domain of Frizzled 8

Method: X-RAY DIFFRACTION Dmax: 88.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Frizzled-8

Mus musculus

UniProt Q61091

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 28–150 Fragment：cysteine-rich domain, UNP residues 28-150 Protein Wnt-8 × 1 （P28026） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 PAM PALMITOLEIC ACID × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；4-10 % (w/v) PEG 400 15-25 mM Zinc acetate 100 mM Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 3.25 Å R-free 0.234

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4F0A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IJY CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MOUSE FRIZZLED 8 (MFZ8) Deposited 2001-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 28–155（128 aa） Fragment：CYSTEINE-RICH DOMAIN
Chain B 28–155（128 aa） Fragment：CYSTEINE-RICH DOMAIN
Mutation：N22E, N125E Mutation：N22E, N125E No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；293 K；Ammonium Sulfate, Hepes, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.35 Å R-free 0.247
6AHY Wnt signaling complex Deposited 2018-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 28–159（132 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CL CHLORIDE ION × 1 PAM PALMITOLEIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES-NaOH (pH 7.5), 0.1 M LiCl, 20%(v/v) Ethylene glycol, 7%(w/v) PEG 4000
Resolution 2.80 Å R-free 0.244
6AHY Wnt signaling complex Deposited 2018-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 28–159（132 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 PAM PALMITOLEIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES-NaOH (pH 7.5), 0.1 M LiCl, 20%(v/v) Ethylene glycol, 7%(w/v) PEG 4000
Resolution 2.80 Å R-free 0.244
6AHY Wnt signaling complex Deposited 2018-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 28–159（132 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M HEPES-NaOH (pH 7.5), 0.1 M LiCl, 20%(v/v) Ethylene glycol, 7%(w/v) PEG 4000
Resolution 2.80 Å R-free 0.244
6TFB Carbamazepine binds Frizzled8 Deposited 2019-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–151（124 aa）
Not recorded GOL GLYCEROL × 2 N6W benzo[b][1]benzazepine-11-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；300 K；0.1 M sodium acetate, pH 5 1 M ammonium sulphate
Resolution 1.68 Å R-free 0.265
6TFB Carbamazepine binds Frizzled8 Deposited 2019-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–151（124 aa）
Not recorded GOL GLYCEROL × 1 N6W benzo[b][1]benzazepine-11-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；300 K；0.1 M sodium acetate, pH 5 1 M ammonium sulphate
Resolution 1.68 Å R-free 0.265
6TFM Frizzled8 CRD Deposited 2019-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–151（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；0.1 M sodium acetate, pH 5 1 M ammonium sulphate
Resolution 2.34 Å R-free 0.300
6TFM Frizzled8 CRD Deposited 2019-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 28–151（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；0.1 M sodium acetate, pH 5 1 M ammonium sulphate
Resolution 2.34 Å R-free 0.300
6TFM Frizzled8 CRD Deposited 2019-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–151（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；0.1 M sodium acetate, pH 5 1 M ammonium sulphate
Resolution 2.34 Å R-free 0.300
6TFM Frizzled8 CRD Deposited 2019-11-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 28–151（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；300 K；0.1 M sodium acetate, pH 5 1 M ammonium sulphate
Resolution 2.34 Å R-free 0.300
8CTG Extracellular architecture of an engineered canonical Wnt signaling ternary complex Deposited 2022-05-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 28–150（123 aa）
Not recorded PAM PALMITOLEIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting before plunging
Resolution 3.80 Å

5 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FZD8_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–123； UniProt 28–150

Protein Wnt-8

Xenopus laevis

UniProt P28026

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 23–338 Fragment：UNP residues 23-338 Frizzled-8 × 1 （Q61091） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 PAM PALMITOLEIC ACID × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.5；293 K；4-10 % (w/v) PEG 400 15-25 mM Zinc acetate 100 mM Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 3.25 Å R-free 0.234

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4F0A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8CTG Extracellular architecture of an engineered canonical Wnt signaling ternary complex Deposited 2022-05-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 22–329（308 aa）
Not recorded PAM PALMITOLEIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；3 s blotting before plunging
Resolution 3.80 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name WNT8_XENLA
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–316； UniProt 23–338

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4f0a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4f0a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4f0a
Deposition date deposition_date2012-05-03
Structure title titleCrystal structure of XWnt8 in complex with the cysteine-rich domain of Frizzled 8
Keywords keywordsWnt signaling, Ligand-receptor complex, Wnt, Frizzled, Fatty acid acylation, Glycosylation, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.32 Å
Radius of gyration Rg (electron density) rg_electron26.91 Å
Forward intensity I(0) i043505300.00
Molecular weight molecular_weight48021.0 kDa
Excluded volume excluded_volume58742 ų
Envelope volume envelope_volume80918 ų
Hydration-shell volume shell_volume25708 ų
Envelope diameter envelope_diameter94.3 Å
Shell Rg shell_rg33.40 Å
Envelope Rg envelope_rg26.24 Å
Shape Rg shape_rg26.90 Å
Total Rg total_rg27.64 Å
Total atoms total_atoms3334
Residues n_residues412
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax88.8 Å
Rg (real space) rg_real27.28 Å
Rg uncertainty (real space) rg_real_error0.51 Å
I(0) (real space) i0_real4.3510e+07
I(0) uncertainty (real space) i0_real_error5.5240e+05
Rg (reciprocal space) rg_reciprocal27.30 Å
I(0) (reciprocal space) i0_reciprocal43510000.0000
Solution quality estimate total_estimate0.9056
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary36.7 Å
Skewness Skewness skewness0.203
Kurtosis Kurtosis kurtosis-0.555
Angular range angular_range— – 0.2900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5136000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.994
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4f0aA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology2000 — Frizzled cysteine-rich domain
Homologous superfamily homologous superfamily10 — Frizzled cysteine-rich domain
Domain ID domain_id4f0aB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology2460 — Endo-n-acetylneuraminidase fold
Homologous superfamily homologous superfamily20 — Wnt (Wingless and Int-1), C-terminal domain
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8. Citations (1)

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9. Files and Curves (10)