SAXSdb — 5un5

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

Frizzled-8

Homo sapiens

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 28–150 Chain B； UniProt 28–150	Fragment：UNP residues 28-150	Designed Wnt agonist B12 × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；295 K；42-49% PEG 400, 0.1 M Tris pH 7.8-8.2, 0.2 M NaCl	Resolution 2.99 Å R-free 0.250

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 5UN5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
21KR A Wnt3a/Fzd8-CRD/LRP6-E3E4 complex with FKBP Deposited 2025-12-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain C 31–155（125 aa） Chain D 31–155（125 aa） Chain G 31–155（125 aa） Chain H 31–155（125 aa） Chain I 31–155（125 aa）	Mutation：C178S Mutation：C178S Mutation：C178S Mutation：C178S Mutation：C178S	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.90 Å
21KS A Wnt3a/Fzd8-CRD/LRP6-E3E4-LA complex with FKBP Deposited 2025-12-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric	Chain C 31–155（125 aa） Chain D 31–155（125 aa） Chain G 31–155（125 aa） Chain H 31–155（125 aa） Chain I 31–155（125 aa）	Mutation：C178S Mutation：C178S Mutation：C178S Mutation：C178S Mutation：C178S	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.01 Å
21KT Wnt3a signalosome extracellular complex Deposited 2025-12-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric	Chain C 31–155（125 aa） Chain D 31–155（125 aa） Chain G 31–155（125 aa） Chain H 31–155（125 aa）	Mutation：Q159A,E161A,C178S,Q221A Mutation：Q159A,E161A,C178S,Q221A Mutation：Q159A,E161A,C178S,Q221A Mutation：Q159A,E161A,C178S,Q221A	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.33 Å
5UN6 Frizzled-8 complex with designed surrogate Wnt agonist, A1 dataset Deposited 2017-01-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–150（123 aa） Fragment：UNP residues 28-150	Mutation：Q22N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20% PEG 3000, 0.1 M Sodium citrate pH 5.5	Resolution 3.20 Å R-free 0.247
5UN6 Frizzled-8 complex with designed surrogate Wnt agonist, A1 dataset Deposited 2017-01-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–150（123 aa） Fragment：UNP residues 28-150	Mutation：Q22N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20% PEG 3000, 0.1 M Sodium citrate pH 5.5	Resolution 3.20 Å R-free 0.247
5UN6 Frizzled-8 complex with designed surrogate Wnt agonist, A1 dataset Deposited 2017-01-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 28–150（123 aa） Fragment：UNP residues 28-150	Mutation：Q22N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20% PEG 3000, 0.1 M Sodium citrate pH 5.5	Resolution 3.20 Å R-free 0.247
5UN6 Frizzled-8 complex with designed surrogate Wnt agonist, A1 dataset Deposited 2017-01-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 28–150（123 aa） Fragment：UNP residues 28-150	Mutation：Q22N	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20% PEG 3000, 0.1 M Sodium citrate pH 5.5	Resolution 3.20 Å R-free 0.247
6NDZ Designed repeat protein in complex with Fz8 Deposited 2018-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 32–150（119 aa）	Mutation：N49Q	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 ACT ACETATE ION × 3 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M ammonium acetate, 0.1 M HEPE, pH 7.5 and 55% MPD	Resolution 2.26 Å R-free 0.238
6NDZ Designed repeat protein in complex with Fz8 Deposited 2018-12-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 32–150（119 aa）	Mutation：N49Q	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M ammonium acetate, 0.1 M HEPE, pH 7.5 and 55% MPD	Resolution 2.26 Å R-free 0.238
6NDZ Designed repeat protein in complex with Fz8 Deposited 2018-12-14	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 32–150（119 aa）	Mutation：N49Q	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M ammonium acetate, 0.1 M HEPE, pH 7.5 and 55% MPD	Resolution 2.26 Å R-free 0.238
8X0T Frizzled8 CRD in complex with pF8_AC3 Fab Deposited 2023-11-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 30–153（124 aa）	Mutation：N49Q	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；32% PEG4000, 0.1 M Tris, pH 8.5, 0.2 M MgCl2	Resolution 2.50 Å R-free 0.290

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

View Construct and Data Evidence

UniProt name	FZD8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–123； UniProt 28–150 Author chain B； PDBConstruct 1–123； UniProt 28–150

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	5un5
Deposition date deposition_date	2017-01-30
Structure title title	Frizzled-8 complex with designed surrogate Wnt agonist, crystal form 1
Keywords keywords	SIGNALING PROTEIN, SIGNALING PROTEIN-De Novo Protein complex; SIGNALING PROTEIN/De Novo 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	32.31 Å
Radius of gyration Rg (electron density) rg_electron	31.81 Å
Forward intensity I(0) i0	34715600.00
Molecular weight molecular_weight	46192.0 kDa
Excluded volume excluded_volume	57888 Å³
Envelope volume envelope_volume	79320 Å³
Hydration-shell volume shell_volume	22799 Å³
Envelope diameter envelope_diameter	110.2 Å
Shell Rg shell_rg	35.46 Å
Envelope Rg envelope_rg	31.42 Å
Shape Rg shape_rg	31.82 Å
Total Rg total_rg	32.14 Å
Total atoms total_atoms	3230
Residues n_residues	417
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	103.3 Å
Rg (real space) rg_real	32.68 Å
Rg uncertainty (real space) rg_real_error	1.00 Å
I(0) (real space) i0_real	3.4720e+07
I(0) uncertainty (real space) i0_real_error	5.9420e+05
Rg (reciprocal space) rg_reciprocal	32.53 Å
I(0) (reciprocal space) i0_reciprocal	34710000.0000
Solution quality estimate total_estimate	0.5961
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.2 Å
Skewness Skewness skewness	0.392
Kurtosis Kurtosis kurtosis	-0.805
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3822000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.744; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.534; Smooth: 0.692

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Frizzled-8
Molecular weight formula_weight	14961.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	3234

ASAKELACQEITVPLCKGIGYQYTYMPNQFNHDTQDEAGLEVHQFWPLVEIQCSPDLKFFLCSMYTPICLEDYKKPLPPCRSVCERAKAGCAPLMRQYGFAWPDRMRCDRLPEQGNPDTLCMDHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Designed Wnt agonist B12
Molecular weight formula_weight	13825.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,C

GGVSFSEVMGKQKDEQAREQLKEGMIKIEEQGKKLSETRTQEELQKYVAAVATFALQAGFLGPNLEERRGFNRRGKEEIGKISGEVYLKLLDLKKAVRAKEKKGLDILNMVGEIKGTLERVYA

来源 Source

来源生物 organism	synthetic construct
NCBI Class编号 ncbi_taxonomy_id	32630
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5un5A00
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	5un5B00
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	41.200 Å
Unit-cell length b length_b	77.510 Å
Unit-cell length c length_c	81.430 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.76 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.994 Å
Low-resolution limit resolution_low	41.152 Å
R factor r_factor	0.2278
R_work r_work	0.2253
R_free r_free	0.2499

fit	/app/data/saxs_computation/un/5un5/5un5.fit
pddf	/app/data/pr_computation/un/5un5/5un5.pr.out
profile	/app/data/saxs_computation/un/5un5/5un5.dat

Frizzled-8 complex with designed surrogate Wnt agonist, crystal form 1

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)