SAXSdb — 8sm5

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

Apoptosis regulator BHRF1

Human herpesvirus 4 strain B95-8

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–157	Not recorded	BID BH3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 mM NaC2H3O2 pH 5.0, 1.6 mM HCOONa	Resolution 2.61 Å R-free 0.260
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 2–157	Not recorded	BID BH3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 mM NaC2H3O2 pH 5.0, 1.6 mM HCOONa	Resolution 2.61 Å R-free 0.260
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 2–157	Not recorded	BID BH3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 mM NaC2H3O2 pH 5.0, 1.6 mM HCOONa	Resolution 2.61 Å R-free 0.260
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 2–157	Not recorded	BID BH3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 mM NaC2H3O2 pH 5.0, 1.6 mM HCOONa	Resolution 2.61 Å R-free 0.260
5	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain I； UniProt 2–157	Not recorded	BID BH3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；277.15 K；0.1 mM NaC2H3O2 pH 5.0, 1.6 mM HCOONa	Resolution 2.61 Å R-free 0.260

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 8SM5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Q59 Solution Structure of the BHRF1 Protein From Epstein-Barr Virus, a Homolog of Human Bcl-2 Deposited 2003-08-06	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–160（160 aa） Fragment：BH1 and BH2 domains	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；303 K；Ionic strength (raw mmCIF value) 20mM；Pressure ambient NMR sample composition U-15N,13C 0.5-1.0 mM BHRF1-EBV-BCL2 , containing 20 mM Tris (pH 7.5) and 2 mM 2H-dithiothreitol \| 90% H2O/10%2H2O	Resolution not provided
2V6Q Crystal Structure of a BHRF-1 : Bim BH3 complex Deposited 2007-07-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–160（160 aa） Fragment：RESIDUES 1-160	Not recorded	BR BROMIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；0.1 M MALIC ACID PH 4.0, 1.7 M NABR, 0.1 M GUANIDINE HCL	Resolution 2.70 Å R-free 0.249
2WH6 Crystal structure of anti-apoptotic BHRF1 in complex with the Bim BH3 domain Deposited 2009-05-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–160（160 aa） Fragment：BCL-2, RESIDUES 1-160	Not recorded	BR BROMIDE ION × 9 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4；0.1 M MALIC ACID PH 4 1.25 M NABR	Resolution 1.50 Å R-free 0.205
2XPX Crystal structure of BHRF1:Bak BH3 complex Deposited 2010-08-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–160（160 aa） Fragment：BCL-2, RESIDUES 1-160	Not recorded	NO3 NITRATE ION × 4 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.4；1.6 M NANO3, 50 MM MALIC ACID PH 4.4	Resolution 2.05 Å R-free 0.217
7P33 Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide Deposited 2021-07-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–160（160 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4M Ammonium phosphate mono basic	Resolution 2.79 Å R-free 0.274
7P33 Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide Deposited 2021-07-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–160（160 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4M Ammonium phosphate mono basic	Resolution 2.79 Å R-free 0.274
7P33 Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide Deposited 2021-07-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–160（160 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4M Ammonium phosphate mono basic	Resolution 2.79 Å R-free 0.274
7P33 Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide Deposited 2021-07-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–160（160 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4M Ammonium phosphate mono basic	Resolution 2.79 Å R-free 0.274
7P33 Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide Deposited 2021-07-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–160（160 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4M Ammonium phosphate mono basic	Resolution 2.79 Å R-free 0.274
7P9W Epstein-Barr virus encoded apoptosis regulator BHRF1 in complex with Puma BH3 Deposited 2021-07-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–160（160 aa）	Not recorded	PO4 PHOSPHATE ION × 3 EDO 1,2-ETHANEDIOL × 6 NH4 AMMONIUM ION × 1 PDO 1,3-PROPANDIOL × 2 MG MAGNESIUM ION × 5 CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4 M Ammonium phosphate monobasic	Resolution 2.00 Å R-free 0.257

6 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EAR_EBVB9
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–156； UniProt 2–157 Author chain C； PDBConstruct 1–156； UniProt 2–157 Author chain E； PDBConstruct 1–156； UniProt 2–157 Author chain G； PDBConstruct 1–156； UniProt 2–157 Author chain I； PDBConstruct 1–156； UniProt 2–157

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	8sm5
Deposition date deposition_date	2023-04-25
Structure title title	Crystal Structure of BHRF1 from Epstein Barr Virus in complex with BID BH3 peptide
Keywords keywords	BHRF1, BID peptide, complex, Viral Protein, BH3 domain, apoptosis; VIRAL PROTEIN
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	31.20 Å
Radius of gyration Rg (electron density) rg_electron	30.17 Å
Forward intensity I(0) i0	158407000.00
Molecular weight molecular_weight	96897.0 kDa
Excluded volume excluded_volume	119970 Å³
Envelope volume envelope_volume	154860 Å³
Hydration-shell volume shell_volume	41990 Å³
Envelope diameter envelope_diameter	100.6 Å
Shell Rg shell_rg	38.06 Å
Envelope Rg envelope_rg	29.79 Å
Shape Rg shape_rg	30.17 Å
Total Rg total_rg	30.83 Å
Total atoms total_atoms	6813
Residues n_residues	848
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	95.4 Å
Rg (real space) rg_real	31.00 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.5840e+08
I(0) uncertainty (real space) i0_real_error	2.1940e+06
Rg (reciprocal space) rg_reciprocal	31.09 Å
I(0) (reciprocal space) i0_reciprocal	158400000.0000
Solution quality estimate total_estimate	0.9048
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.0 Å
Skewness Skewness skewness	0.085
Kurtosis Kurtosis kurtosis	-0.535
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	119800000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.965

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Apoptosis regulator BHRF1
Molecular weight formula_weight	17918.2 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I
Atom count atom_count	6850

AYSTREILLALCIRDSRVHGNGTLHPVLELAARETPLRLSPEDTVVLRYHVLLEEIIERNSETFTETWNRFITHTEHVDLDFNSVFLEIFHRGDPSLGRALAWMAWCMHACRTLCCNQSTPYYVVDLSVRGMLEASEGLDGWIHQQGGWSTLIEDN

来源 Source

来源生物 organism	Human herpesvirus 4 strain B95-8
通用名 common_name	Epstein-Barr virus (strain B95-8), Human herpesvirus 4 (strain B95-8)
NCBI Class编号 ncbi_taxonomy_id	10377
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	BID BH3
Molecular weight formula_weight	2027.3 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

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

DIIRNIARHLAQVGDSMD

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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8. Citations (1)

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Unit-cell length a length_a	186.817 Å
Unit-cell length b length_b	186.817 Å
Unit-cell length c length_c	70.486 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	30

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	hexagonal

Resolution resolution	2.610 Å
Low-resolution limit resolution_low	80.894 Å
R factor r_factor	0.2007
R_work r_work	0.1976
R_free r_free	0.2597

fit	/app/data/saxs_computation/sm/8sm5/8sm5.fit
pddf	/app/data/pr_computation/sm/8sm5/8sm5.pr.out
profile	/app/data/saxs_computation/sm/8sm5/8sm5.dat

Crystal Structure of BHRF1 from Epstein Barr Virus in complex with BID BH3 peptide

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

Apoptosis regulator BHRF1

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)