SAXSdb — 3dvu

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Beclin-1 × 1 （Q14457） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Beclin-1 × 1 （Q14457） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P89884_MHV68
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–137； UniProt 2–136 Author chain B； PDBConstruct 3–137； UniProt 2–136

Beclin-1

OrganismNot specified

UniProt Q14457

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	V-bcl-2 × 1 （P89884） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	V-bcl-2 × 1 （P89884） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BECN1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–26； UniProt 105–130 Author chain D； PDBConstruct 1–26； UniProt 105–130

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	3dvu
Deposition date deposition_date	2008-07-20
Structure title title	Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and the Beclin 1 BH3 domain
Keywords keywords	;AUTOPHAGY, PROTEIN-PROTEIN COMPLEX, VIRAL BCL-2, BECLIN 1, APOPTOSIS, M11, ANTIVIRAL DEFENSE, BH3 DOMAIN, Coiled coil, Cytoplasm, Golgi apparatus, Membrane, Polymorphism, Viral Protein-apoptosis COMPLEX ;; Viral Protein/apoptosis
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3dvu__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3dvu__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dvu__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	16.17 Å
Rg (electron density)	14.65 Å
Total Rg	15.96 Å
Atom count	1246
Residues	155
Excluded volume	22213 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dvu__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3dvu__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	V-bcl-2
Molecular weight formula_weight	16652.9 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	2578

MASHKKSGTYWATLITAFLKTVSKVEELDCVDSAVLVDVSKIITLTQEFRRHYDSVYRADYGPALKNWKRDLSKLFTSLFVDVINSGRIVGFFDVGRYVCEEVLCPGSWTEDHELLNDCMTHFFIENNLMNHFPLEDHHHHHH

Source Source

Source organism organism	Murid herpesvirus 4
Common name common_name	MuHV-4
NCBI taxonomy ID ncbi_taxonomy_id	33708
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Beclin-1
Molecular weight formula_weight	2845.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

DGGTMENLSRRLKVTGDLFDIMSGQT

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	94

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3dvua_
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	d3dvub_
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	3dvuA00
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	3dvuB00
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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Unit-cell length a length_a	44.424 Å
Unit-cell length b length_b	53.134 Å
Unit-cell length c length_c	64.059 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.67 °
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	2.500 Å
Low-resolution limit resolution_low	19.700 Å
R factor r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.2610

Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and the Beclin 1 BH3 domain

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3dvu__assembly_2__model_1

3dvu__assembly_2__model_1 | I(q)

3dvu__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and the Beclin 1 BH3 domain

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

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Beclin-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3dvu__assembly_2__model_1

3dvu__assembly_2__model_1 | I(q)

3dvu__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)