SAXSdb — 4jm0

▼

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 Homooligomer Protein × 2 其他Polymer 5 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 30–279 Chain B； UniProt 30–279	Fragment：UL141 ECTODOMAIN, UNP residues 30-279	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5	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

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 4JM0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 A 32–246（215 aa） Fragment：UL141, UNP residues 32-246 Chain B 32–246（215 aa） Fragment：UL141, UNP residues 32-246	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
9DIX HCMV gH/UL116/UL141 3-mer complex, ectodomain Deposited 2024-09-06	Different construct 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 1–250； UniProt 30–279 Author chain B； PDBConstruct 1–250； UniProt 30–279

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4jm0
Deposition date deposition_date	2013-03-13
Structure title title	Structure of Human Cytomegalovirus Immune Modulator UL141
Keywords keywords	;viral protein in complex with human receptor, Immunoglobulin-like V-set folg of N-terminal domain; Ig-like beta sandwich domain, viral immunomodulator, host-virus interaction, TRAIL-R2, CD155, glycosylation, membrane, CELL ADHESION ;; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	22.42 Å
Radius of gyration Rg (electron density) rg_electron	21.23 Å
Forward intensity I(0) i0	28437700.00
Molecular weight molecular_weight	40679.0 kDa
Excluded volume excluded_volume	50767 Å³
Envelope volume envelope_volume	62471 Å³
Hydration-shell volume shell_volume	24195 Å³
Envelope diameter envelope_diameter	79.9 Å
Shell Rg shell_rg	28.37 Å
Envelope Rg envelope_rg	21.76 Å
Shape Rg shape_rg	21.25 Å
Total Rg total_rg	22.11 Å
Total atoms total_atoms	2863
Residues n_residues	358
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	82.5 Å
Rg (real space) rg_real	22.38 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	2.8440e+07
I(0) uncertainty (real space) i0_real_error	4.2560e+05
Rg (reciprocal space) rg_reciprocal	22.39 Å
I(0) (reciprocal space) i0_reciprocal	28440000.0000
Solution quality estimate total_estimate	0.7582
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	26.2 Å
Skewness Skewness skewness	0.332
Kurtosis Kurtosis kurtosis	-0.206
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10980000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.629; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.964; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4jm0A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3790 —

Domain ID domain_id	4jm0B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	3790 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	96.060 Å
Unit-cell length b length_b	96.060 Å
Unit-cell length c length_c	136.071 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.250 Å
Low-resolution limit resolution_low	11.980 Å
R factor r_factor	0.2010
R_work r_work	0.2010
R_free r_free	0.2790

Description description	Protein UL141
Molecular weight formula_weight	29419.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2863

Structure of Human Cytomegalovirus Immune Modulator UL141

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

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 branched

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/jm/4jm0/4jm0.fit
pddf	/app/data/pr_computation/jm/4jm0/4jm0.pr.out
profile	/app/data/saxs_computation/jm/4jm0/4jm0.dat