SAXSdb — 4cdk

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 53–205	Fragment：ECTODOMAIN, RESIDUES 53-205	R-SPONDIN-1 × 1 （Q2MKA7）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 53–205	Fragment：ECTODOMAIN, RESIDUES 53-205	R-SPONDIN-1 × 1 （Q2MKA7）	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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 53–205	Fragment：ECTODOMAIN, RESIDUES 53-205	R-SPONDIN-1 × 1 （Q2MKA7）	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
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 53–205	Fragment：ECTODOMAIN, RESIDUES 53-205	R-SPONDIN-1 × 1 （Q2MKA7）	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

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 4CDK	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 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 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 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 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 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 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 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 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 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 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
4CDJ Structure of ZNRF3 ectodomain Deposited 2013-11-01	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 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	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
4CDJ Structure of ZNRF3 ectodomain Deposited 2013-11-01	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 53–205（153 aa） Fragment：ECTODOMAIN, RESIDUES 53-205	Not recorded	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
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 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 14 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 Author chain C； PDBConstruct 3–155； UniProt 53–205 Author chain D； PDBConstruct 3–155； UniProt 53–205

R-SPONDIN-1

HOMO SAPIENS

UniProt Q2MKA7

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 31–145	Fragment：FURIN-LIKE DOMAIN, RESIDUES 31-145	E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 × 1 （Q5SSZ7）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 31–145	Fragment：FURIN-LIKE DOMAIN, RESIDUES 31-145	E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 × 1 （Q5SSZ7）	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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain H； UniProt 31–145	Fragment：FURIN-LIKE DOMAIN, RESIDUES 31-145	E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 × 1 （Q5SSZ7）	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
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 31–145	Fragment：FURIN-LIKE DOMAIN, RESIDUES 31-145	E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 × 1 （Q5SSZ7）	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

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 4CDK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4BSO Crystal structure of R-spondin 1 (Fu1Fu2) - Native Deposited 2013-06-11	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 31–146（116 aa） Fragment：FU1FU2, RESIDUES 31-146	Not recorded	EDO 1,2-ETHANEDIOL × 5 CL CHLORIDE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.250
4BSP Crystal structure of R-spondin 1 (Fu1Fu2) - Holmium soak Deposited 2013-06-11	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 31–146（116 aa） Fragment：FU1FU2, RESIDUES 31-146	Not recorded	HO HOLMIUM ATOM × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.260
4BSR Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P22121 crystal form Deposited 2013-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 31–146（116 aa） Fragment：FU1FU2, RESIDUES 31-146 Chain D 31–146（116 aa） Fragment：FU1FU2, RESIDUES 31-146	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.258
4BSS Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P21 crystal form Deposited 2013-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 31–146（116 aa） Fragment：FU1FU2, RESIDUES 31-146 Chain D 31–146（116 aa） Fragment：FU1FU2, RESIDUES 31-146	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.290
4BSS Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P21 crystal form Deposited 2013-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 31–146（116 aa） Fragment：FU1FU2, RESIDUES 31-146 Chain H 31–146（116 aa） Fragment：FU1FU2, RESIDUES 31-146	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.290
4BST Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P6122 crystal form Deposited 2013-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 31–146（116 aa） Fragment：FU1FU2, RESIDUES 31-146 Chain D 31–146（116 aa） Fragment：FU1FU2, RESIDUES 31-146	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 4.30 Å R-free 0.268
4BSU Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in C2 crystal form Deposited 2013-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain G 31–146（116 aa） Chain H 31–146（116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.287
4BSU Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in C2 crystal form Deposited 2013-06-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 31–146（116 aa） Chain D 31–146（116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.20 Å R-free 0.287
4KNG Crystal structure of human LGR5-RSPO1-RNF43 Deposited 2013-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain M 35–144（110 aa） Fragment：furin repeats Chain P 35–144（110 aa） Fragment：furin repeats	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10% PEG4000, 0.2M ammonium sulfate, 7% Sucrose and 0.1 M TRIS pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.50 Å R-free 0.276
4KT1 Complex of R-spondin 1 with LGR4 extracellular domain Deposited 2013-05-19	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 E 39–128（90 aa） Fragment：UNP residues 39-128	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；291 K；PEG, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 2.50 Å R-free 0.209
4LI2 Crystal Structures of Lgr4 and its complex with R-spondin1 Deposited 2013-07-02	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 33–144（112 aa） Fragment：FU 1 and FU 2 repeat residues 33-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.7；298 K；22% PEG3350, 200 mM MgCl2 and 100 mM BisTris pH 5.7, vapor diffusion, temperature 298K	Resolution 3.19 Å R-free 0.284
4QXF crystal structure of human LGR4 and Rspo1 Deposited 2014-07-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 34–135（102 aa） Fragment：UNP residues 34-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M MES pH 6.5, 0.2M sodium thiocyanate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.25 Å R-free 0.243
4QXF crystal structure of human LGR4 and Rspo1 Deposited 2014-07-20	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 34–135（102 aa） Fragment：UNP residues 34-135	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；289 K；0.1M MES pH 6.5, 0.2M sodium thiocyanate, 22% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.25 Å R-free 0.243
8WVU Cryo-EM structure of LGR4 in complex with Rspo1 and RNF43 Deposited 2023-10-24	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 35–144（110 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen PROPANE	Resolution 3.61 Å

11 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RSPO1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 3–117； UniProt 31–145 Author chain F； PDBConstruct 3–117； UniProt 31–145 Author chain G； PDBConstruct 3–117； UniProt 31–145 Author chain H； PDBConstruct 3–117； UniProt 31–145

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	4cdk
Deposition date deposition_date	2013-11-01
Structure title title	Structure of ZNRF3-RSPO1
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	34.49 Å
Radius of gyration Rg (electron density) rg_electron	33.48 Å
Forward intensity I(0) i0	216478000.00
Molecular weight molecular_weight	113330.0 kDa
Excluded volume excluded_volume	140320 Å³
Envelope volume envelope_volume	198670 Å³
Hydration-shell volume shell_volume	48858 Å³
Envelope diameter envelope_diameter	130.4 Å
Shell Rg shell_rg	40.47 Å
Envelope Rg envelope_rg	33.46 Å
Shape Rg shape_rg	33.42 Å
Total Rg total_rg	34.23 Å
Total atoms total_atoms	7896
Residues n_residues	1040
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	124.2 Å
Rg (real space) rg_real	34.39 Å
Rg uncertainty (real space) rg_real_error	1.35 Å
I(0) (real space) i0_real	2.1650e+08
I(0) uncertainty (real space) i0_real_error	3.7010e+06
Rg (reciprocal space) rg_reciprocal	34.45 Å
I(0) (reciprocal space) i0_reciprocal	216500000.0000
Solution quality estimate total_estimate	0.8335
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.9 Å
Skewness Skewness skewness	0.273
Kurtosis Kurtosis kurtosis	-0.028
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23670000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.625; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.956

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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	E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
Molecular weight formula_weight	17986.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7982

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 polymer

Description description	R-SPONDIN-1
Molecular weight formula_weight	13706.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

GSRISAEGSQACAKGCELCSEVNGCLKCSPKLFILLERNDIRQVGVCLPSCPPGYFDARNPDMNKCIKCKIEHCEACFSHNFCTKCKEGLYLHKGRCYPACPEGSSAANGTMECSSPAAAHHHHHH

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HHUMA
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	HOMO SAPIENS

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	55

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4cdke_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.9 — Growth factor receptor domain
Family Family family	g.3.9.1 — Growth factor receptor domain

Domain ID domain_id	d4cdkf_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.9 — Growth factor receptor domain
Family Family family	g.3.9.1 — Growth factor receptor domain

Domain ID domain_id	d4cdkg_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.9 — Growth factor receptor domain
Family Family family	g.3.9.1 — Growth factor receptor domain

Domain ID domain_id	d4cdkh_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.9 — Growth factor receptor domain
Family Family family	g.3.9.1 — Growth factor receptor domain

CATH v4.4 (8 domains)

Domain ID domain_id	4cdkA00
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	4cdkB00
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	4cdkC00
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	4cdkD00
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	4cdkE00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily	10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2

Domain ID domain_id	4cdkF00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily	10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2

Domain ID domain_id	4cdkG00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily	10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2

Domain ID domain_id	4cdkH00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily	10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2

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8. Citations (1)

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Unit-cell length a length_a	51.700 Å
Unit-cell length b length_b	80.160 Å
Unit-cell length c length_c	82.980 Å
Unit-cell angle α angle_alpha	66.27 °
Unit-cell angle β angle_beta	81.36 °
Unit-cell angle γ angle_gamma	80.66 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	44.706 Å
R factor r_factor	0.2192
R_work r_work	0.2177
R_free r_free	0.2464

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

Structure of ZNRF3-RSPO1

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

R-SPONDIN-1

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) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)