SAXSdb — 4c8w

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

R-SPONDIN-2

XENOPUS (SILURANA) TROPICALIS

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 I； UniProt 35–144	Fragment：FU1-FU2, RESIDUES 35-144	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.10 Å R-free 0.313
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain J； UniProt 35–144	Fragment：FU1-FU2, RESIDUES 35-144	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 3.10 Å R-free 0.313

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 4C8W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4C8V Xenopus RSPO2 Fu1-Fu2 crystal form I Deposited 2013-10-01	Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.270
4C8V Xenopus RSPO2 Fu1-Fu2 crystal form I Deposited 2013-10-01	Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.270
4C8V Xenopus RSPO2 Fu1-Fu2 crystal form I Deposited 2013-10-01	Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.270
4C8V Xenopus RSPO2 Fu1-Fu2 crystal form I Deposited 2013-10-01	Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.270
4C8V Xenopus RSPO2 Fu1-Fu2 crystal form I Deposited 2013-10-01	Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.270
4C8V Xenopus RSPO2 Fu1-Fu2 crystal form I Deposited 2013-10-01	Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.270
4C8V Xenopus RSPO2 Fu1-Fu2 crystal form I Deposited 2013-10-01	Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.270
4C8V Xenopus RSPO2 Fu1-Fu2 crystal form I Deposited 2013-10-01	Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.270
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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 32–152（121 aa） Fragment：FU1-FU2, RESIDUES 32-152 Chain D 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 32-152	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	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 structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144 Chain D 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	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 structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144 Chain H 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.334
4C9R Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 crystal form I Deposited 2013-10-02	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144 Chain D 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.246
4C9U Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 crystal form II Deposited 2013-10-03	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.310
4C9U Xenopus ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 crystal form II Deposited 2013-10-03	Different oligomeric state Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å R-free 0.310
4C9V Xenopus RNF43 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 Deposited 2013-10-03	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 35–144（110 aa） Fragment：FU1-FU2, RESIDUES 35-144	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å R-free 0.395

6 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RSPO2_XENTR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain I； PDBConstruct 4–113； UniProt 35–144 Author chain J； PDBConstruct 4–113； UniProt 35–144

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	4c8w
Deposition date deposition_date	2013-10-01
Structure title title	Xenopus RSPO2 Fu1-Fu2 crystal form II
Keywords keywords	SIGNALING PROTEIN, WNT, ZNRF3, RNF43, LGR4, LGR5, LGR6, RSPO, R-SPO, RSPO1, RSPO3, RSPO4, RECEPTOR, MEMBRANE, SIGNALLING; 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	22.98 Å
Radius of gyration Rg (electron density) rg_electron	22.43 Å
Forward intensity I(0) i0	10736900.00
Molecular weight molecular_weight	22488.0 kDa
Excluded volume excluded_volume	27228 Å³
Envelope volume envelope_volume	37251 Å³
Hydration-shell volume shell_volume	15001 Å³
Envelope diameter envelope_diameter	74.5 Å
Shell Rg shell_rg	27.46 Å
Envelope Rg envelope_rg	22.35 Å
Shape Rg shape_rg	22.42 Å
Total Rg total_rg	23.16 Å
Total atoms total_atoms	1549
Residues n_residues	208
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	71.8 Å
Rg (real space) rg_real	23.00 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	1.0740e+07
I(0) uncertainty (real space) i0_real_error	1.7080e+05
Rg (reciprocal space) rg_reciprocal	23.00 Å
I(0) (reciprocal space) i0_reciprocal	10740000.0000
Solution quality estimate total_estimate	0.7467
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	0.178
Kurtosis Kurtosis kurtosis	-0.793
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	529700.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.976; Stabil: 1.000; Sysdev: 0.307; Positv: 1.000; Valcen: 0.881; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4c8wi_
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.3.9.0 — automated matches

Domain ID domain_id	d4c8wj_
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.3.9.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	4c8wI00
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	4c8wJ00
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	87.122 Å
Unit-cell length b length_b	87.122 Å
Unit-cell length c length_c	76.951 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	16

Space group space_group	P 4 2 2
Space-group number int_tables_number	89
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	87.120 Å
R factor r_factor	0.2336
R_work r_work	0.2298
R_free r_free	0.3128

Description description	R-SPONDIN-2
Molecular weight formula_weight	13781.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J
Atom count atom_count	1549

Xenopus RSPO2 Fu1-Fu2 crystal form II

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

R-SPONDIN-2

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

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	XENOPUS (SILURANA) TROPICALIS
通用名 common_name	WESTERN CLAWED FROG
NCBI Class编号 ncbi_taxonomy_id	8364
宿主生物 host_organism	HOMO SAPIENS

fit	/app/data/saxs_computation/c8/4c8w/4c8w.fit
pddf	/app/data/pr_computation/c8/4c8w/4c8w.pr.out
profile	/app/data/saxs_computation/c8/4c8w/4c8w.dat