SAXSdb — 4cdj

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

E3 UBIQUITIN-PROTEIN LIGASE ZNRF3

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 53–205	Fragment：ECTODOMAIN, RESIDUES 53-205	EDO 1,2-ETHANEDIOL × 3 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：0.2 M AMMONIUM FORMATE AT PH 6.6 WITH 20% W/V PEG3350	Resolution 1.50 Å R-free 0.177
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 53–205	Fragment：ECTODOMAIN, RESIDUES 53-205	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：0.2 M AMMONIUM FORMATE AT PH 6.6 WITH 20% W/V PEG3350	Resolution 1.50 Å R-free 0.177

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 4CDJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4C86 mouse ZNRF3 ectodomain crystal form I Deposited 2013-09-30	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 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205 Chain B 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.276
4C8A mouse ZNRF3 ectodomain crystal form II Deposited 2013-09-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å R-free 0.299
4C8A mouse ZNRF3 ectodomain crystal form II Deposited 2013-09-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205 Chain B 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å R-free 0.299
4C8C mouse ZNRF3 ectodomain crystal form III Deposited 2013-09-30	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 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205 Chain B 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.320
4C8F mouse ZNRF3 ectodomain crystal form IV Deposited 2013-09-30	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 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205 Chain D 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.69 Å R-free 0.341
4C8F mouse ZNRF3 ectodomain crystal form IV Deposited 2013-09-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205 Chain C 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.69 Å R-free 0.341
4C8P mouse ZNRF3 ectodomain crystal form V, disulfide-bridged S90C variant Deposited 2013-10-01	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 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.286
4C99 Mouse ZNRF3 ectodomain in complex with mouse RSPO2 Fu1-Fu2 crystal form I Deposited 2013-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205 Chain C 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.323
4C9A Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form I Deposited 2013-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–165（165 aa） Fragment：ECTODOMAIN, RESIDUES 1-165 Chain C 1–165（165 aa） Fragment：ECTODOMAIN, RESIDUES 1-165	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.273
4C9E Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form II Deposited 2013-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205 Chain C 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.334
4C9E Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form II Deposited 2013-10-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205 Chain G 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.334
4CDK Structure of ZNRF3-RSPO1 Deposited 2013-11-01	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 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.2M SODIUM BROMIDE AND 20% W/V PEG 3350	Resolution 2.80 Å R-free 0.246
4CDK Structure of ZNRF3-RSPO1 Deposited 2013-11-01	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 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.2M SODIUM BROMIDE AND 20% W/V PEG 3350	Resolution 2.80 Å R-free 0.246
4CDK Structure of ZNRF3-RSPO1 Deposited 2013-11-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.2M SODIUM BROMIDE AND 20% W/V PEG 3350	Resolution 2.80 Å R-free 0.246
4CDK Structure of ZNRF3-RSPO1 Deposited 2013-11-01	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.2M SODIUM BROMIDE AND 20% W/V PEG 3350	Resolution 2.80 Å R-free 0.246
4UFS Low resolution structure R-spondin-2 (Fu1Fu2) in complex with the ectodomains of LGR5 and ZNRF3 Deposited 2015-03-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.100 M AMMONIUM ACETATE, 0.600 M SODIUM CHLORIDE, 0.050 M MES PH 6.0, 0.005 M MAGNESIUM SULPHATE	Resolution 4.80 Å R-free 0.313

10 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ZNRF3_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–155； UniProt 53–205 Author chain B； PDBConstruct 3–155； UniProt 53–205

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	4cdj
Deposition date deposition_date	2013-11-01
Structure title title	Structure of ZNRF3 ectodomain
Keywords keywords	LIGASE, WNT SIGNALING, ADULT STEM CELLS, E3 LIGASE, PROTEASE-ASSOCIATED DOMAIN, ZINC RING FINGER, LGR5, R-SPONDIN; LIGASE
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	21.58 Å
Radius of gyration Rg (electron density) rg_electron	20.49 Å
Forward intensity I(0) i0	20583100.00
Molecular weight molecular_weight	33906.0 kDa
Excluded volume excluded_volume	42358 Å³
Envelope volume envelope_volume	50850 Å³
Hydration-shell volume shell_volume	21015 Å³
Envelope diameter envelope_diameter	74.4 Å
Shell Rg shell_rg	26.89 Å
Envelope Rg envelope_rg	20.79 Å
Shape Rg shape_rg	20.47 Å
Total Rg total_rg	21.46 Å
Total atoms total_atoms	4715
Residues n_residues	307
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	72.4 Å
Rg (real space) rg_real	21.59 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	2.0580e+07
I(0) uncertainty (real space) i0_real_error	2.8460e+05
Rg (reciprocal space) rg_reciprocal	21.59 Å
I(0) (reciprocal space) i0_reciprocal	20580000.0000
Solution quality estimate total_estimate	0.7951
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.399
Kurtosis Kurtosis kurtosis	-0.200
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4524000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.783; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
Molecular weight formula_weight	17986.3 kDa
EC 编号 ec_number	6.3.2.-
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	5184

GSKETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHLAAAHHHHHH

来源 Source

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	HOMO SAPIENS

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	296

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4cdjA00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4cdjB00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

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8. Citations (1)

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Unit-cell length a length_a	35.686 Å
Unit-cell length b length_b	73.503 Å
Unit-cell length c length_c	58.573 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.49 °
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	1.500 Å
Low-resolution limit resolution_low	45.567 Å
R factor r_factor	0.1625
R_work r_work	0.1616
R_free r_free	0.1773

fit	/app/data/saxs_computation/cd/4cdj/4cdj.fit
pddf	/app/data/pr_computation/cd/4cdj/4cdj.pr.out
profile	/app/data/saxs_computation/cd/4cdj/4cdj.dat

Structure of ZNRF3 ectodomain

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

E3 UBIQUITIN-PROTEIN LIGASE ZNRF3

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