SAXSdb — 1ijy

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1. Protein Identity and Related Structures Protein Identity & Related Structures

FRIZZLED HOMOLOG 8

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 28–155 Chain B； UniProt 28–155	Fragment：CYSTEINE-RICH DOMAIN Mutation：N22E, N125E	No other associated polymer	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

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 1IJY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4F0A Crystal structure of XWnt8 in complex with the cysteine-rich domain of Frizzled 8 Deposited 2012-05-03	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 28–150（123 aa） Fragment：cysteine-rich domain, UNP residues 28-150	Not recorded	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
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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 3–130； UniProt 28–155 Author chain B； PDBConstruct 3–130； UniProt 28–155

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ijy
Deposition date deposition_date	2001-05-01
Structure title title	CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MOUSE FRIZZLED 8 (MFZ8)
Keywords keywords	WNT RECEPTOR, FRIZZLED PROTEIN STRUCTURE, CYSTEINE-RICH, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.53 Å
Radius of gyration Rg (electron density) rg_electron	21.10 Å
Forward intensity I(0) i0	14968500.00
Molecular weight molecular_weight	28375.0 kDa
Excluded volume excluded_volume	35095 Å³
Envelope volume envelope_volume	42347 Å³
Hydration-shell volume shell_volume	17741 Å³
Envelope diameter envelope_diameter	71.1 Å
Shell Rg shell_rg	26.40 Å
Envelope Rg envelope_rg	21.30 Å
Shape Rg shape_rg	21.15 Å
Total Rg total_rg	21.67 Å
Total atoms total_atoms	1978
Residues n_residues	244
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	72.2 Å
Rg (real space) rg_real	21.61 Å
Rg uncertainty (real space) rg_real_error	0.60 Å
I(0) (real space) i0_real	1.4970e+07
I(0) uncertainty (real space) i0_real_error	2.1760e+05
Rg (reciprocal space) rg_reciprocal	21.60 Å
I(0) (reciprocal space) i0_reciprocal	14970000.0000
Solution quality estimate total_estimate	0.8710
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	70.0 Å
Skewness Skewness skewness	0.409
Kurtosis Kurtosis kurtosis	-0.445
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2654000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.893; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1ijya_
Class class	a — All alpha proteins
Fold Fold fold	a.141 — Frizzled cysteine-rich domain
Superfamily Superfamily superfamily	a.141.1 — Frizzled cysteine-rich domain
Family Family family	a.141.1.1 — Frizzled cysteine-rich domain

Domain ID domain_id	d1ijyb_
Class class	a — All alpha proteins
Fold Fold fold	a.141 — Frizzled cysteine-rich domain
Superfamily Superfamily superfamily	a.141.1 — Frizzled cysteine-rich domain
Family Family family	a.141.1.1 — Frizzled cysteine-rich domain

CATH v4.4 (2 domains)

Domain ID domain_id	1ijyA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	2000 — Frizzled cysteine-rich domain
Homologous superfamily homologous superfamily	10 — Frizzled cysteine-rich domain

Domain ID domain_id	1ijyB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	2000 — Frizzled cysteine-rich domain
Homologous superfamily homologous superfamily	10 — Frizzled cysteine-rich domain

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8. Citations (1)

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Unit-cell length a length_a	55.690 Å
Unit-cell length b length_b	36.370 Å
Unit-cell length c length_c	57.940 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.82 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	1.350 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2250
R_free r_free	0.2470

Description description	FRIZZLED HOMOLOG 8
Molecular weight formula_weight	14943.1 kDa
Mutation mutation	N22E, N125E
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2257

CRYSTAL STRUCTURE OF THE CYSTEINE-RICH DOMAIN OF MOUSE FRIZZLED 8 (MFZ8)

1. Protein Identity and Related Structures Protein Identity & Related Structures

FRIZZLED HOMOLOG 8

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Cricetulus griseus

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	279

fit	/app/data/saxs_computation/ij/1ijy/1ijy.fit
pddf	/app/data/pr_computation/ij/1ijy/1ijy.pr.out
profile	/app/data/saxs_computation/ij/1ijy/1ijy.dat