SAXSdb — 5cir

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

Tumor necrosis factor ligand superfamily member 10

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 114–281 Chain B； UniProt 114–281 Chain D； UniProt 114–281	Fragment：Residues 114-281	Tumor necrosis factor receptor superfamily member 10A × 3 （O00220） ZN ZINC ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；100 mM MMT (1:2:2 ratio of DL-malic acid, MES, Tris base), pH 5.0, 22.2%(W/V) PEG 2000MME	Resolution 3.00 Å R-free 0.216

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 5CIR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D0G CRYSTAL STRUCTURE OF DEATH RECEPTOR 5 (DR5) BOUND TO APO2L/TRAIL Deposited 1999-09-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 114–281（168 aa） Fragment：RESIDUES 114-281 Chain B 114–281（168 aa） Fragment：RESIDUES 114-281 Chain D 114–281（168 aa） Fragment：RESIDUES 114-281	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；15% Peg8K, 10% ethylene glycol, 0.2M ammonium sulface, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 19K	Resolution 2.40 Å R-free 0.267
1D2Q CRYSTAL STRUCTURE OF HUMAN TRAIL Deposited 1999-09-27	Different construct Different mutation/modification 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 114–281（168 aa） Fragment：EXTRA CELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 9；295 K；PEG 550 MME, bicine pH 9.0, cadmium chloride, EVAPORATION, temperature 22K	Resolution 2.80 Å R-free 0.282
1D2Q CRYSTAL STRUCTURE OF HUMAN TRAIL Deposited 1999-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain B 114–281（168 aa） Fragment：EXTRA CELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 9；295 K；PEG 550 MME, bicine pH 9.0, cadmium chloride, EVAPORATION, temperature 22K	Resolution 2.80 Å R-free 0.282
1D2Q CRYSTAL STRUCTURE OF HUMAN TRAIL Deposited 1999-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 114–281（168 aa） Fragment：EXTRA CELLULAR DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 9；295 K；PEG 550 MME, bicine pH 9.0, cadmium chloride, EVAPORATION, temperature 22K	Resolution 2.80 Å R-free 0.282
1D4V Crystal structure of trail-DR5 complex Deposited 1999-10-06	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 119–281（163 aa） Fragment：SINGLE SUBUNIT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；25% ETHYLENE GLYCOL, 0.1% N-OCTYL-BETA-GLUCOSIDE, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 20K	Resolution 2.20 Å R-free 0.270
1DG6 CRYSTAL STRUCTURE OF APO2L/TRAIL Deposited 1999-11-23	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 91–281（191 aa） Fragment：TRIMERIC JELLY-ROLL DOMAIN OF APO2L	Mutation：D218A	ZN ZINC ION × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；WELL SOLUTION 32% MPD; DROP 1.2MG/ML APO2L, 20MM TRIS HCL PH 7.5, 1% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.30 Å R-free 0.197
1DU3 Crystal structure of TRAIL-SDR5 Deposited 2000-01-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 114–281（168 aa） Chain E 114–281（168 aa） Chain F 114–281（168 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.6；295 K；PEG 1000, Sodium Acetate, Sodium Chloride, pH 4.6, EVAPORATION, temperature 22K	Resolution 2.20 Å R-free 0.291
1DU3 Crystal structure of TRAIL-SDR5 Deposited 2000-01-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain J 114–281（168 aa） Chain K 114–281（168 aa） Chain L 114–281（168 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.6；295 K；PEG 1000, Sodium Acetate, Sodium Chloride, pH 4.6, EVAPORATION, temperature 22K	Resolution 2.20 Å R-free 0.291
4N90 Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody Deposited 2013-10-18	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 C 114–281（168 aa） Fragment：UNP residues 114-281	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris pH 8.0, 1.0 M LiCl, 0.2 M MnCl2, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.286
4N90 Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody Deposited 2013-10-18	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 B 114–281（168 aa） Fragment：UNP residues 114-281	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris pH 8.0, 1.0 M LiCl, 0.2 M MnCl2, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.286
4N90 Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody Deposited 2013-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 114–281（168 aa） Fragment：UNP residues 114-281	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris pH 8.0, 1.0 M LiCl, 0.2 M MnCl2, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.286

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

View Construct and Data Evidence

UniProt name	TNF10_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–169； UniProt 114–281 Author chain B； PDBConstruct 2–169； UniProt 114–281 Author chain D； PDBConstruct 2–169； UniProt 114–281

Tumor necrosis factor receptor superfamily member 10A

Homo sapiens

UniProt O00220

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 E； UniProt 125–232 Chain F； UniProt 125–232 Chain G； UniProt 125–232	Fragment：Extracellular domain residues 125-232	Tumor necrosis factor ligand superfamily member 10 × 3 （P50591） ZN ZINC ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；100 mM MMT (1:2:2 ratio of DL-malic acid, MES, Tris base), pH 5.0, 22.2%(W/V) PEG 2000MME	Resolution 3.00 Å R-free 0.216

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	TR10A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–108； UniProt 125–232 Author chain F； PDBConstruct 1–108； UniProt 125–232 Author chain G； PDBConstruct 1–108； UniProt 125–232

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	5cir
Deposition date deposition_date	2015-07-13
Structure title title	Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10)
Keywords keywords	Apoptosis, binding and specificity, ligand-receptor complex, TNF receptor family; APOPTOSIS
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	27.40 Å
Radius of gyration Rg (electron density) rg_electron	25.88 Å
Forward intensity I(0) i0	113852000.00
Molecular weight molecular_weight	80000.0 kDa
Excluded volume excluded_volume	98179 Å³
Envelope volume envelope_volume	122480 Å³
Hydration-shell volume shell_volume	37701 Å³
Envelope diameter envelope_diameter	88.1 Å
Shell Rg shell_rg	34.86 Å
Envelope Rg envelope_rg	26.44 Å
Shape Rg shape_rg	25.81 Å
Total Rg total_rg	26.95 Å
Total atoms total_atoms	5603
Residues n_residues	752
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	85.6 Å
Rg (real space) rg_real	27.20 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	1.1390e+08
I(0) uncertainty (real space) i0_real_error	1.7720e+06
Rg (reciprocal space) rg_reciprocal	27.26 Å
I(0) (reciprocal space) i0_reciprocal	113900000.0000
Solution quality estimate total_estimate	0.8987
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.4 Å
Skewness Skewness skewness	0.106
Kurtosis Kurtosis kurtosis	-0.498
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12770000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Tumor necrosis factor ligand superfamily member 10
Molecular weight formula_weight	19652.0 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	5611

MVRERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Tumor necrosis factor receptor superfamily member 10A
Molecular weight formula_weight	11749.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

HSPLGELCPPGSHRSERPGACNRCTEGVGYTNASNNLFACLPCTACKSDEEERSPCTTTRNTACQCKPGTFRNDNSAEMCRKCSTGCPRGMVKVKDCTPWSDIECVHK

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	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5cira_
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	d5cirb_
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	d5cird_
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 (9 domains)

Domain ID domain_id	5cirA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	5cirB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	5cirD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	5cirE01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	5cirE02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	5cirF01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	5cirF02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	5cirG01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

Domain ID domain_id	5cirG02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	50 — Tumor Necrosis Factor Receptor, subunit A; domain 2
Homologous superfamily homologous superfamily	10 — Tumor Necrosis Factor Receptor, subunit A, domain 2

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8. Citations (1)

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Unit-cell length a length_a	84.600 Å
Unit-cell length b length_b	87.600 Å
Unit-cell length c length_c	107.700 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	27.600 Å
R factor r_factor	0.1792
R_work r_work	0.1767
R_free r_free	0.2163

fit	/app/data/saxs_computation/ci/5cir/5cir.fit
pddf	/app/data/pr_computation/ci/5cir/5cir.pr.out
profile	/app/data/saxs_computation/ci/5cir/5cir.dat

Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10)

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

Tumor necrosis factor ligand superfamily member 10

State in the Current Structure

Other States of the Same Protein in the Database

Tumor necrosis factor receptor superfamily member 10A

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)