4n90

Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody

Method: X-RAY DIFFRACTION D_max: 168.5 Å Quality: GOOD

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

Tumor necrosis factor receptor superfamily member 10B

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain T； UniProt 57–182	Fragment：UNP residues 57-182	Tumor necrosis factor ligand superfamily member 10 × 1 （P50591） Fab light chain × 1 Fab heavy chain × 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain S； UniProt 57–182	Fragment：UNP residues 57-182	Tumor necrosis factor ligand superfamily member 10 × 1 （P50591） Fab light chain × 1 Fab heavy chain × 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
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain R； UniProt 57–182	Fragment：UNP residues 57-182	Tumor necrosis factor ligand superfamily member 10 × 1 （P50591） Fab light chain × 1 Fab heavy chain × 1 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

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 4N90	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 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 R 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN RESIDUES 1-130 Chain S 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN RESIDUES 1-130 Chain T 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN RESIDUES 1-130	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
1DU3 Crystal structure of TRAIL-SDR5 Deposited 2000-01-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN Chain C 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN	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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN Chain H 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN Chain I 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN	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
1ZA3 The crystal structure of the YSd1 Fab bound to DR5 Deposited 2005-04-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 54–183（130 aa） Fragment：Extra-cellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；292 K；20% PEG 8000, 0.2M MgAcetate, 0.1M NaCacodylate pH 6.2-6.6, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.35 Å R-free 0.280
1ZA3 The crystal structure of the YSd1 Fab bound to DR5 Deposited 2005-04-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 54–183（130 aa） Fragment：Extra-cellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；292 K；20% PEG 8000, 0.2M MgAcetate, 0.1M NaCacodylate pH 6.2-6.6, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.35 Å R-free 0.280
2H9G Crystal structure of phage derived Fab BdF1 with human Death Receptor 5 (DR5) Deposited 2006-06-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 54–183（130 aa） Fragment：extra cellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；Crystals from drops containing an equal volume of protein and well solution consisting of 20% PEG 3350, 0.2M Na2HPO4, 0.1 M Bis-Tris, pH 6.1-6.8. The crystals were cryo-protected with well solution supplemented with 20% PEG 200., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.32 Å R-free 0.282
2H9G Crystal structure of phage derived Fab BdF1 with human Death Receptor 5 (DR5) Deposited 2006-06-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 54–183（130 aa） Fragment：extra cellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；Crystals from drops containing an equal volume of protein and well solution consisting of 20% PEG 3350, 0.2M Na2HPO4, 0.1 M Bis-Tris, pH 6.1-6.8. The crystals were cryo-protected with well solution supplemented with 20% PEG 200., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.32 Å R-free 0.282
3X3F TRAIL-R2 Extracellular Region Complexed to a Fab fragment from Human Agonist Antibody KMTR2 Deposited 2015-01-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 54–184（131 aa） Fragment：UNP residues 54-184	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；7.5% PEG 3350, 75mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.224
4I9X Crystal structure of human cytomegalovirus glycoprotein UL141 targeting the death receptor TRAIL-R2 Deposited 2012-12-05	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 58–184（127 aa） Fragment：TRAIL-R2, UNP residues 58-184 Chain D 58–184（127 aa） Fragment：TRAIL-R2, UNP residues 58-184	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；295.15 K；20% PEG 8K, CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K	Resolution 2.10 Å R-free 0.274
4OD2 Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5 Deposited 2014-01-09	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 73–183（111 aa） Fragment：UNP residues 73-183	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；Protein (7mg/mL in 20 mM Tris-HCl, 150 mM NaCl) was mixed with equal volume of well solution (30% PEG 4K, 0.1 M Tris-HCl pH 8.5, 0.2M MgCl2), VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.20 Å R-free 0.305
6NHW Structure of the transmembrane domain of the Death Receptor 5 - Dimer of Trimer Deposited 2018-12-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 208–242（35 aa） Fragment：residues 208-242 Chain B 208–242（35 aa） Fragment：residues 208-242 Chain C 208–242（35 aa） Fragment：residues 208-242 Chain D 208–242（35 aa） Fragment：residues 208-242 Chain E 208–242（35 aa） Fragment：residues 208-242 Chain F 208–242（35 aa） Fragment：residues 208-242	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.8 mM [U-13C; U-15N; 85%-2H] Transmembrane Domain of Death Receptor 5, 50 mM DMPC, 100 mM DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.8 mM [U-13C; U-15N] Transmembrane Domain of Death Receptor 5, 50 mM [acyl chain U-2H] DMPC, 100 mM [acyl chain U-2H] DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.4 mM [U-15N; U-2H; 15%-13C] Transmembrane Domain of Death Receptor 5, 50 mM [acyl chain U-2H] DMPC, 100 mM [acyl chain U-2H] DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6NHY Structure of the transmembrane domain of the Death Receptor 5 mutant (G217Y) - Trimer Only Deposited 2018-12-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 208–242（35 aa） Chain B 208–242（35 aa） Chain C 208–242（35 aa）	Mutation：G217Y Mutation：G217Y Mutation：G217Y	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.8 mM [U-13C; U-15N; 85%-2H] Transmembrane Domain of DR5 Mutant G217Y, 50 mM DMPC, 100 mM DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.8 mM [U-13C; U-15N] Transmembrane Domain of DR5 Mutant G217Y, 50 mM [acyl chain U-2H] DMPC, 100 mM [acyl chain U-2H] DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.4 mM [15%-13C; U-15N; H-2H] Transmembrane Domain of DR5 Mutant G217Y, 50 mM [acyl chain U-2H] DMPC, 100 mM [acyl chain U-2H] DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6T3J Dual Epitope Targeting by Anti-DR5 Antibodies Deposited 2019-10-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 58–184（127 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；281 K；10% (w/v) PEG 4000 200 mM ammonium sulphate 100 mM Sodium acetate pH 4.6	Resolution 3.05 Å R-free 0.282
6T3J Dual Epitope Targeting by Anti-DR5 Antibodies Deposited 2019-10-11	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 58–184（127 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；281 K；10% (w/v) PEG 4000 200 mM ammonium sulphate 100 mM Sodium acetate pH 4.6	Resolution 3.05 Å R-free 0.282
8DPX Preligand association structure of DR5 Deposited 2022-07-17	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 77–184（108 aa） Chain B 77–184（108 aa） Chain C 77–184（108 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.2；310 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 400 uM [U-100% 15N, U-100% 13C, U-85% 2H] DR5 ectodomain, 4.4 mM DGS-NTA (Ni), 44 mM DMPC, 88 mM D7PC, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 500 uM [U-100% 15N; U-100% 2H] DR5 ectodomain, 5.5 mM DGS-NTA (Ni), 55 mM DMPC, 110 mM D7PC, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 250 uM [U-100% 15N; U-100% 2H] Isotopically mixed DR5 ectodomain, 250 uM [U-100% 13C] DR5 ectodomain, 5.5 mM DGS-NTA (Ni), 55 mM DMPC, 110 mM D7PC, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 250 uM [U-100% 13C; U-100% 15N; U-95% 2H] Isotopically mixed DR5 ectodomain, 250 uM DR5 ectodomain, 5.5 mM DGS-NTA (Ni), 55 mM DMPC, 110 mM D7PC, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 500 uM [U-100% 13C; U-100% 15N] DR5 ectodomain, 5.5 mM DGS-NTA (Ni), 55 mM DMPC, 110 mM D7PC, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 400 uM [U-100% 15N, U-85% 2H] DR5 ectodomain, 4.4 mM DGS-NTA (Ni), 44 mM DMPC, 88 mM D7PC, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	TR10B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain R； PDBConstruct 1–126； UniProt 57–182 Author chain S； PDBConstruct 1–126； UniProt 57–182 Author chain T； PDBConstruct 1–126； UniProt 57–182

Tumor necrosis factor ligand superfamily member 10

Homo sapiens

UniProt P50591

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 114–281	Fragment：UNP residues 114-281	Tumor necrosis factor receptor superfamily member 10B × 1 （O14763） Fab light chain × 1 Fab heavy chain × 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
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 114–281	Fragment：UNP residues 114-281	Tumor necrosis factor receptor superfamily member 10B × 1 （O14763） Fab light chain × 1 Fab heavy chain × 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
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 114–281	Fragment：UNP residues 114-281	Tumor necrosis factor receptor superfamily member 10B × 1 （O14763） Fab light chain × 1 Fab heavy chain × 1 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 4N90	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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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
5CIR Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10) Deposited 2015-07-13	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 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 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

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TNF10_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–168； UniProt 114–281 Author chain B； PDBConstruct 1–168； UniProt 114–281 Author chain C； PDBConstruct 1–168； UniProt 114–281

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4n90
Deposition date deposition_date	2013-10-18
Structure title title	Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody
Keywords keywords	DR5, TRAIL, Agonist, antibody, cooperation, clustering, Apoptosis-Immune System complex; Apoptosis/Immune System
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	48.47 Å
Radius of gyration Rg (electron density) rg_electron	48.98 Å
Forward intensity I(0) i0	802729000.00
Molecular weight molecular_weight	226470.0 kDa
Excluded volume excluded_volume	280030 Å³
Envelope volume envelope_volume	406260 Å³
Hydration-shell volume shell_volume	72723 Å³
Envelope diameter envelope_diameter	166.8 Å
Shell Rg shell_rg	48.50 Å
Envelope Rg envelope_rg	49.65 Å
Shape Rg shape_rg	48.99 Å
Total Rg total_rg	48.91 Å
Total atoms total_atoms	15927
Residues n_residues	2074
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	168.5 Å
Rg (real space) rg_real	48.67 Å
Rg uncertainty (real space) rg_real_error	1.56 Å
I(0) (real space) i0_real	8.0270e+08
I(0) uncertainty (real space) i0_real_error	1.3830e+07
Rg (reciprocal space) rg_reciprocal	48.47 Å
I(0) (reciprocal space) i0_reciprocal	802500000.0000
Solution quality estimate total_estimate	0.8717
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	51.1 Å
Skewness Skewness skewness	0.382
Kurtosis Kurtosis kurtosis	-0.458
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	108500000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.857

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5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Tumor necrosis factor receptor superfamily member 10B
Molecular weight formula_weight	14193.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R,S,T
Atom count atom_count	15934

TQQDLAPQQRAAPQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDIECVHKE

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 ligand superfamily member 10
Molecular weight formula_weight	19520.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C

VRERGPQRVAAHITGTRGRSNTLSSPNSKNEKALGRKINSWESSRSGHSFLSNLHLRNGELVIHEKGFYYIYSQTYFRFQEEIKENTKNDKQMVQYIYKYTSYPDPILLMKSARNSCWSKDAEYGLYSIYQGGIFELKENDRIFVSVTNEHLIDMDHEASFFGAFLVG

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 polymer

Description description	Fab light chain
Molecular weight formula_weight	23415.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

EIVLTQSPGTLSLSPGERATLSCRASQGISRSYLAWYQQKPGQAPSLLIYGASSRATGIPDRFSGSGSGTDFTLTISRLEPEDFAVYYCQQFGSSPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606

Entity 4 Entity 4 polymer

Description description	Fab heavy chain
Molecular weight formula_weight	23774.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

QVQLQESGPGLVKPSQTLSLTCTVSGGSISSGDYFWSWIRQLPGKGLEWIGHIHNSGTTYYNPSLKSRVTISVDTSKKQFSLRLSSVTAADTAVYYCARDRGGDYYYGMDVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606

Entity 5 Entity 5 non-polymer

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

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7. Fold Classification (SCOP + CATH) 21 domains

CATH v4.4 (21 domains)

Domain ID domain_id	4n90A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4n90B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4n90C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4n90D01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90D02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90E01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90E02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90F01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90F02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90G01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90G02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90I01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90I02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4n90R01
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	4n90R02
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	4n90S01
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	4n90S02
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	4n90T01
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	4n90T02
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	152.006 Å
Unit-cell length b length_b	152.006 Å
Unit-cell length c length_c	613.155 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2290
R_free r_free	0.2860

fit	/app/data/saxs_computation/n9/4n90/4n90.fit
pddf	/app/data/pr_computation/n9/4n90/4n90.pr.out
profile	/app/data/saxs_computation/n9/4n90/4n90.dat

Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody

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

Tumor necrosis factor receptor superfamily member 10B

State in the Current Structure

Other States of the Same Protein in the Database

Tumor necrosis factor ligand superfamily member 10

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 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

7. Fold Classification (SCOP + CATH) 21 domains

CATH v4.4 (21 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)