SAXSdb — 3k48

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

Tumor necrosis factor ligand superfamily member 13

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 104–241 Chain B； UniProt 104–241 Chain D； UniProt 104–241	Fragment：residues 104-241	peptide × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；292 K；2ul drops of protein (5 mg/mg. at pH 9.7) was added to 2 uL of 4M formate. Crystals formed immediately, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.80 Å R-free 0.267

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 3K48	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1U5X Crystal structure of murine APRIL at pH 5.0 Deposited 2004-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 104–241（138 aa） Fragment：TNF domain of murine APRIL	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；292 K；0.1 M Citric Acid, 1.0 M LiCL, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 1.80 Å R-free 0.256
1U5Y Crystal structure of murine APRIL, pH 8.0 Deposited 2004-07-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 104–241（138 aa） Fragment：TNF domain of murine APRIL Chain B 104–241（138 aa） Fragment：TNF domain of murine APRIL Chain D 104–241（138 aa） Fragment：TNF domain of murine APRIL	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292 K；0.1 M Tris pH 8.0, 1M LiCl, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.30 Å R-free 0.268
1U5Z The Crystal structure of murine APRIL, pH 8.5 Deposited 2004-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 104–241（138 aa） Fragment：TNF domain of murine APRIL	Not recorded	NI NICKEL (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；292 K；0.1 M Tris, pH 8.5, 0.5 M KSCN, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.40 Å R-free 0.265
1XU1 The crystal structure of APRIL bound to TACI Deposited 2004-10-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 104–241（138 aa） Fragment：TNF domain of murine APRIL Chain B 104–241（138 aa） Fragment：TNF domain of murine APRIL Chain D 104–241（138 aa） Fragment：TNF domain of murine APRIL	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；well solution: 70% MPD, 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 1.90 Å R-free 0.203
1XU2 The crystal structure of APRIL bound to BCMA Deposited 2004-10-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 104–241（138 aa） Fragment：TNF domain of APRIL Chain B 104–241（138 aa） Fragment：TNF domain of APRIL Chain D 104–241（138 aa） Fragment：TNF domain of APRIL	Not recorded	NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；292 K；well solution: 0.1M MES, 5% Peg 8000, 10% Peg 1000, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.35 Å R-free 0.213

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TNF13_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–140； UniProt 104–241 Author chain B； PDBConstruct 3–140； UniProt 104–241 Author chain D； PDBConstruct 3–140； UniProt 104–241

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	3k48
Deposition date deposition_date	2009-10-05
Structure title title	Crystal structure of APRIL bound to a peptide
Keywords keywords	cytokine, TNFSF, Cleavage on pair of basic residues, Disulfide bond, Glycoprotein, Immune response, Secreted; CYTOKINE
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	22.08 Å
Radius of gyration Rg (electron density) rg_electron	20.54 Å
Forward intensity I(0) i0	44382400.00
Molecular weight molecular_weight	51336.0 kDa
Excluded volume excluded_volume	64098 Å³
Envelope volume envelope_volume	73299 Å³
Hydration-shell volume shell_volume	27942 Å³
Envelope diameter envelope_diameter	67.4 Å
Shell Rg shell_rg	28.81 Å
Envelope Rg envelope_rg	21.01 Å
Shape Rg shape_rg	20.52 Å
Total Rg total_rg	21.55 Å
Total atoms total_atoms	3613
Residues n_residues	453
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	67.5 Å
Rg (real space) rg_real	21.87 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	4.4380e+07
I(0) uncertainty (real space) i0_real_error	5.0680e+05
Rg (reciprocal space) rg_reciprocal	21.91 Å
I(0) (reciprocal space) i0_reciprocal	44380000.0000
Solution quality estimate total_estimate	0.8976
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.2 Å
Skewness Skewness skewness	0.041
Kurtosis Kurtosis kurtosis	-0.539
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15390000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Tumor necrosis factor ligand superfamily member 13
Molecular weight formula_weight	15705.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D
Atom count atom_count	3613

GSKKHSVLHLVPVNITSKADSDVTEVMWQPVLRRGRGLEAQGDIVRVWDTGIYLLYSQVLFHDVTFTMGQVVSREGQGRRETLFRCIRSMPSDPDRAYNSCYSAGVFHLHQGDIITVKIPRANAKLSLSPHGTFLGFVKL

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	peptide
Molecular weight formula_weight	2031.3 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,S,T

SGWCDPRWYDPFMCEH

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3k48a_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d3k48b_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

Domain ID domain_id	d3k48d_
Class class	b — All beta proteins
Fold Fold fold	b.22 — TNF-like
Superfamily Superfamily superfamily	b.22.1 — TNF-like
Family Family family	b.22.1.1 — TNF-like

CATH v4.4 (3 domains)

Domain ID domain_id	3k48A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3k48B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	3k48D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	100.811 Å
Unit-cell length b length_b	84.771 Å
Unit-cell length c length_c	55.562 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.45 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2117
R_work r_work	0.2055
R_free r_free	0.2669

fit	/app/data/saxs_computation/k4/3k48/3k48.fit
pddf	/app/data/pr_computation/k4/3k48/3k48.pr.out
profile	/app/data/saxs_computation/k4/3k48/3k48.dat

Crystal structure of APRIL bound to a peptide

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

Tumor necrosis factor ligand superfamily member 13

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)