SAXSdb — 6tfb

▼

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

Frizzled-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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 28–151	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 28–151	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

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 6TFB	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
4F0A Crystal structure of XWnt8 in complex with the cysteine-rich domain of Frizzled 8 Deposited 2012-05-03	Different construct 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
6TFM Frizzled8 CRD Deposited 2019-11-14	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 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 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 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 10 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 4–127； UniProt 28–151 Author chain B； PDBConstruct 4–127； UniProt 28–151

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6tfb
Deposition date deposition_date	2019-11-13
Structure title title	Carbamazepine binds Frizzled8
Keywords keywords	Wnt receptor Frizzled8 carbamazepine, ONCOPROTEIN; ONCOPROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	21.34 Å
Radius of gyration Rg (electron density) rg_electron	20.82 Å
Forward intensity I(0) i0	16336700.00
Molecular weight molecular_weight	30112.0 kDa
Excluded volume excluded_volume	37459 Å³
Envelope volume envelope_volume	44962 Å³
Hydration-shell volume shell_volume	18613 Å³
Envelope diameter envelope_diameter	71.1 Å
Shell Rg shell_rg	26.39 Å
Envelope Rg envelope_rg	20.93 Å
Shape Rg shape_rg	20.85 Å
Total Rg total_rg	21.52 Å
Total atoms total_atoms	2103
Residues n_residues	253
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

▼

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

Maximum dimension Dmax dmax	70.9 Å
Rg (real space) rg_real	21.39 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	1.6340e+07
I(0) uncertainty (real space) i0_real_error	2.1040e+05
Rg (reciprocal space) rg_reciprocal	21.39 Å
I(0) (reciprocal space) i0_reciprocal	16340000.0000
Solution quality estimate total_estimate	0.8722
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.415
Kurtosis Kurtosis kurtosis	-0.388
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4634000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.928

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Frizzled-8
Molecular weight formula_weight	15815.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2179

ETGASAKELACQEITVPLCKGIGYEYTYMPNQFNHDTQDEAGLEVHQFWPLVEIQCSPDLKFFLCSMYTPICLEDYKKPLPPCRSVCERAKAGCAPLMRQYGFAWPDRMRCDRLPEQGNPDTLCMDYERGTLEVLFQG

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	benzo[b][1]benzazepine-11-carboxamide
Molecular weight formula_weight	236.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6tfba1
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	d6tfba2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6tfbb1
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	d6tfbb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

▶

8. Citations (1)

▶

Unit-cell length a length_a	52.002 Å
Unit-cell length b length_b	68.143 Å
Unit-cell length c length_c	73.818 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.680 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2005
R_free r_free	0.2654

fit	/app/data/saxs_computation/tf/6tfb/6tfb.fit
pddf	/app/data/pr_computation/tf/6tfb/6tfb.pr.out
profile	/app/data/saxs_computation/tf/6tfb/6tfb.dat

Carbamazepine binds Frizzled8

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

Frizzled-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