SAXSdb — 3bl2

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

V-bcl-2

Murid herpesvirus 4

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 5–135	Fragment：UNP residues 5-135	Beclin-1 × 1 （O88597）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% PEG 3350, 0.2M MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.247
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 5–135	Fragment：UNP residues 5-135	Beclin-1 × 1 （O88597）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% PEG 3350, 0.2M MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.247
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 5–135 Chain B； UniProt 5–135	Fragment：UNP residues 5-135	Beclin-1 × 2 （O88597）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% PEG 3350, 0.2M MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.247

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 3BL2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ABO NMR structure of gamma herpesvirus 68 a viral Bcl-2 homolog Deposited 2005-07-15	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 1–136（136 aa） Fragment：truncated Bcl-2 homolog	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.8；303 K；Ionic strength (raw mmCIF value) 20mM Tris；Pressure ambient NMR sample composition .1 mM HV68-viral BCL2 U-15N, 13C, 20mM Tris; 90% H2O, 10% D2O \| 100% D2O NMR sample composition .5 mM HV68-viral BCL2 U-15N, 13C, 75% 2H ; 20mM Tris; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
3DVU Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and the Beclin 1 BH3 domain Deposited 2008-07-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–136（135 aa） Fragment：residues 2-136	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；20% PEG 3350, 0.1M sodium acetate, pH 4.5, 10mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.261
3DVU Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and the Beclin 1 BH3 domain Deposited 2008-07-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–136（135 aa） Fragment：residues 2-136	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；20% PEG 3350, 0.1M sodium acetate, pH 4.5, 10mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.261
4MI8 Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and a Beclin 1 BH3 domain-derived peptide Deposited 2013-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–136（135 aa） Fragment：UNP residues 2-136	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2.5 M ammonium sulfate, 8% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.224
4MI8 Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and a Beclin 1 BH3 domain-derived peptide Deposited 2013-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–136（135 aa） Fragment：UNP residues 2-136	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2.5 M ammonium sulfate, 8% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.224
4MI8 Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and a Beclin 1 BH3 domain-derived peptide Deposited 2013-08-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 2–136（135 aa） Fragment：UNP residues 2-136 Chain B 2–136（135 aa） Fragment：UNP residues 2-136	Not recorded	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；2.5 M ammonium sulfate, 8% 2-propanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.224

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

View Construct and Data Evidence

UniProt name	P89884_MHV68
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 5–135 Author chain B； PDBConstruct 1–131； UniProt 5–135

Beclin-1

Mus musculus

UniProt O88597

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 C； UniProt 106–124	Fragment：BCL-2 binding region, BH3-like domain, UNP residues 106-124	V-bcl-2 × 1 （P89884）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% PEG 3350, 0.2M MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.247
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 106–124	Fragment：BCL-2 binding region, BH3-like domain, UNP residues 106-124	V-bcl-2 × 1 （P89884）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% PEG 3350, 0.2M MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.247
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 106–124 Chain D； UniProt 106–124	Fragment：BCL-2 binding region, BH3-like domain, UNP residues 106-124	V-bcl-2 × 2 （P89884）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；25% PEG 3350, 0.2M MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.247

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 3BL2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5YR0 Structure of Beclin1-UVRAG coiled coil domain complex Deposited 2017-11-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 174–223（50 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M citric acid pH 3.5, 3.0M sodium chloride	Resolution 1.90 Å R-free 0.195

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BECN1_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–19； UniProt 106–124 Author chain D； PDBConstruct 1–19； UniProt 106–124

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	3bl2
Deposition date deposition_date	2007-12-10
Structure title title	Crystal Structure of M11, the BCL-2 Homolog of Murine Gamma-herpesvirus 68, Complexed with Mouse Beclin1 (residues 106-124)
Keywords keywords	;protein-protein complex, viral BCL-2, Beclin1, apoptosis, M11, autophagy, Antiviral defense, Coiled coil, Cytoplasm, Golgi apparatus, Membrane, VIRAL PROTEIN-APOPTOSIS COMPLEX ;; VIRAL PROTEIN/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	24.85 Å
Radius of gyration Rg (electron density) rg_electron	24.41 Å
Forward intensity I(0) i0	19981200.00
Molecular weight molecular_weight	34738.0 kDa
Excluded volume excluded_volume	43700 Å³
Envelope volume envelope_volume	52590 Å³
Hydration-shell volume shell_volume	19295 Å³
Envelope diameter envelope_diameter	87.5 Å
Shell Rg shell_rg	29.80 Å
Envelope Rg envelope_rg	24.77 Å
Shape Rg shape_rg	24.37 Å
Total Rg total_rg	25.24 Å
Total atoms total_atoms	2444
Residues n_residues	300
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	86.7 Å
Rg (real space) rg_real	25.16 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	1.9980e+07
I(0) uncertainty (real space) i0_real_error	3.3090e+05
Rg (reciprocal space) rg_reciprocal	25.09 Å
I(0) (reciprocal space) i0_reciprocal	19980000.0000
Solution quality estimate total_estimate	0.6913
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.551
Kurtosis Kurtosis kurtosis	-0.429
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13170000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.502; Stabil: 0.988; Sysdev: 1.000; Positv: 1.000; Valcen: 0.511; Smooth: 0.000

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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	V-bcl-2
Molecular weight formula_weight	15152.2 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	2503

KSGTYWATLITAFLKTVSKVEELDCVDSAVLVDVSKIITLTQEFRRHYDSVYRADYGPALKNWKRDLSKLFTSLFVDVINSGRIVGFFDVGRYVCEEVLCPGSWTEDHELLNDCMTHFFIENNLMNHFPLE

来源 Source

来源生物 organism	Murid herpesvirus 4
通用名 common_name	Murine herpesvirus 68
NCBI Class编号 ncbi_taxonomy_id	33708
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Beclin-1
Molecular weight formula_weight	2242.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

TMENLSRRLKVTGDLFDIM

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	59

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3bl2a_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.1 — Toxins' membrane translocation domains
Superfamily Superfamily superfamily	f.1.4 — Bcl-2 inhibitors of programmed cell death
Family Family family	f.1.4.1 — Bcl-2 inhibitors of programmed cell death

Domain ID domain_id	d3bl2b_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.1 — Toxins' membrane translocation domains
Superfamily Superfamily superfamily	f.1.4 — Bcl-2 inhibitors of programmed cell death
Family Family family	f.1.4.1 — Bcl-2 inhibitors of programmed cell death

CATH v4.4 (2 domains)

Domain ID domain_id	3bl2A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	437 — Apoptosis Regulator Bcl-x
Homologous superfamily homologous superfamily	10 — Blc2-like

Domain ID domain_id	3bl2B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	437 — Apoptosis Regulator Bcl-x
Homologous superfamily homologous superfamily	10 — Blc2-like

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8. Citations (1)

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Unit-cell length a length_a	42.863 Å
Unit-cell length b length_b	53.601 Å
Unit-cell length c length_c	73.586 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2040
R_free r_free	0.2470

fit	/app/data/saxs_computation/bl/3bl2/3bl2.fit
pddf	/app/data/pr_computation/bl/3bl2/3bl2.pr.out
profile	/app/data/saxs_computation/bl/3bl2/3bl2.dat

Crystal Structure of M11, the BCL-2 Homolog of Murine Gamma-herpesvirus 68, Complexed with Mouse Beclin1 (residues 106-124)

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

V-bcl-2

State in the Current Structure

Other States of the Same Protein in the Database

Beclin-1

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

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)