SAXSdb — 4i9x

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

Protein UL141

Human herpesvirus 5

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 32–246 Chain B； UniProt 32–246	Fragment：UL141, UNP residues 32-246 Non-standard monomer：Yes (specific site not provided by mmCIF)	Tumor necrosis factor receptor superfamily member 10B × 2 （O14763） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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

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 4I9X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4JM0 Structure of Human Cytomegalovirus Immune Modulator UL141 Deposited 2013-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–279（250 aa） Fragment：UL141 ECTODOMAIN, UNP residues 30-279 Chain B 30–279（250 aa） Fragment：UL141 ECTODOMAIN, UNP residues 30-279	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；295.15 K；0.2 M calcium acetate, 0.1 M imidazole pH 8, 10% (w/v) polyethylene glycol 8000, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K	Resolution 3.25 Å R-free 0.279
9DIX HCMV gH/UL116/UL141 3-mer complex, ectodomain Deposited 2024-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 30–279（250 aa） Chain E 30–279（250 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.51 Å
9DIY Local Cryo-EM structure of HCMV gH/UL116 interaction Deposited 2024-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 30–279（250 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.36 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	UL141_HCMVM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–215； UniProt 32–246 Author chain B； PDBConstruct 1–215； UniProt 32–246

Tumor necrosis factor receptor superfamily member 10B

Homo sapiens

UniProt O14763

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 58–184 Chain D； UniProt 58–184	Fragment：TRAIL-R2, UNP residues 58-184 Non-standard monomer：Yes (specific site not provided by mmCIF)	Protein UL141 × 2 （Q6RJQ3） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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

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 4I9X	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 ligand/ion 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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification 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
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 T 57–182（126 aa） Fragment：UNP residues 57-182	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 S 57–182（126 aa） Fragment：UNP residues 57-182	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 R 57–182（126 aa） Fragment：UNP residues 57-182	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
4OD2 Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5 Deposited 2014-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 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 ligand/ion 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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TR10B_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–127； UniProt 58–184 Author chain D； PDBConstruct 1–127； UniProt 58–184

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	4i9x
Deposition date deposition_date	2012-12-05
Structure title title	Crystal structure of human cytomegalovirus glycoprotein UL141 targeting the death receptor TRAIL-R2
Keywords keywords	Ig-like domain, APOPTOSIS; 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	27.94 Å
Radius of gyration Rg (electron density) rg_electron	26.80 Å
Forward intensity I(0) i0	85386800.00
Molecular weight molecular_weight	67858.0 kDa
Excluded volume excluded_volume	82642 Å³
Envelope volume envelope_volume	106410 Å³
Hydration-shell volume shell_volume	32726 Å³
Envelope diameter envelope_diameter	86.1 Å
Shell Rg shell_rg	34.63 Å
Envelope Rg envelope_rg	27.19 Å
Shape Rg shape_rg	26.80 Å
Total Rg total_rg	27.57 Å
Total atoms total_atoms	4685
Residues n_residues	572
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	85.3 Å
Rg (real space) rg_real	27.86 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	8.5390e+07
I(0) uncertainty (real space) i0_real_error	1.2170e+06
Rg (reciprocal space) rg_reciprocal	27.89 Å
I(0) (reciprocal space) i0_reciprocal	85390000.0000
Solution quality estimate total_estimate	0.9127
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.198
Kurtosis Kurtosis kurtosis	-0.667
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17420000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.955

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Protein UL141
Molecular weight formula_weight	25106.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4933

PFATADIAEKMWAENYETTSPAPVLVAEGEQVTIPCTVMTHSWPMVSIRARFCRSHDGSDELILDAVKGHRLMNGLQYRLPYATWNFSQLHLGQIFSLTFNVSTDTAGMYECVLRNYSHGLIMQRFVILTQLETLSRPDEPCCTPALGRYSLGDQIWSPTPWRLRNHDCGMYRGFQRNYFYIGRADAEDCWKPACPDEEPDRCWTVIQRYRLPGD

来源 Source

来源生物 organism	Human herpesvirus 5
通用名 common_name	HHV-5
NCBI Class编号 ncbi_taxonomy_id	295027
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Tumor necrosis factor receptor superfamily member 10B
Molecular weight formula_weight	14330.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

QQDLAPQQRAAPQQKRSSPSEGLCPPGHHISEDGRDCISCKYGQDYSTHWNDLLFCLRCTRCDSGEVELSPCTTTRNTVCQCEEGTFREEDSPEMCRKCRTGCPRGMVKVGDCTPWSDIECVHKESG

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	Spodoptera frugiperda

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	239

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4i9xc1
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.0 — automated matches

Domain ID domain_id	d4i9xc2
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.0 — automated matches

Domain ID domain_id	d4i9xc3
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.0 — automated matches

Domain ID domain_id	d4i9xd1
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.0 — automated matches

Domain ID domain_id	d4i9xd2
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.0 — automated matches

Domain ID domain_id	d4i9xd3
Class class	g — Small proteins
Fold Fold fold	g.24 — TNF receptor-like
Superfamily Superfamily superfamily	g.24.1 — TNF receptor-like
Family Family family	g.24.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	4i9xA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3790 —

Domain ID domain_id	4i9xB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3790 —

Domain ID domain_id	4i9xC01
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	4i9xC02
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	4i9xD01
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	4i9xD02
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	67.916 Å
Unit-cell length b length_b	97.043 Å
Unit-cell length c length_c	141.422 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	8

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	19.830 Å
R factor r_factor	0.2240
R_work r_work	0.2230
R_free r_free	0.2742

fit	/app/data/saxs_computation/i9/4i9x/4i9x.fit
pddf	/app/data/pr_computation/i9/4i9x/4i9x.pr.out
profile	/app/data/saxs_computation/i9/4i9x/4i9x.dat

Crystal structure of human cytomegalovirus glycoprotein UL141 targeting the death receptor TRAIL-R2

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

Protein UL141

State in the Current Structure

Other States of the Same Protein in the Database

Tumor necrosis factor receptor superfamily member 10B

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)