4ldb

Crystal Structure of Ebola Virus VP40 Dimer

Method: X-RAY DIFFRACTION

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

Matrix protein VP40

Ebola virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VP40_EBOZM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–297； UniProt 44–326 Author chain B； PDBConstruct 15–297； UniProt 44–326 Author chain C； PDBConstruct 15–297； UniProt 44–326 Author chain D； PDBConstruct 15–297； UniProt 44–326

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	4ldb
Deposition date deposition_date	2013-06-24
Structure title title	Crystal Structure of Ebola Virus VP40 Dimer
Keywords keywords	viral matrix protein, viral budding, assembly, viral transcription regulation, VIRAL PROTEIN; VIRAL PROTEIN
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.

4ldb__assembly_1__model_1

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

Download this curve (.dat)

4ldb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ldb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.82 Å
Rg (electron density)	27.31 Å
Total Rg	28.16 Å
Atom count	3838
Residues	501
Excluded volume	69594 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ldb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ldb__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 (1)

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4ldba1
Class class	b — All beta proteins
Fold Fold fold	b.31 — EV matrix protein
Superfamily Superfamily superfamily	b.31.1 — EV matrix protein
Family Family family	b.31.1.1 — EV matrix protein

Domain ID domain_id	d4ldba2
Class class	b — All beta proteins
Fold Fold fold	b.31 — EV matrix protein
Superfamily Superfamily superfamily	b.31.1 — EV matrix protein
Family Family family	b.31.1.1 — EV matrix protein

Domain ID domain_id	d4ldbb1
Class class	b — All beta proteins
Fold Fold fold	b.31 — EV matrix protein
Superfamily Superfamily superfamily	b.31.1 — EV matrix protein
Family Family family	b.31.1.1 — EV matrix protein

Domain ID domain_id	d4ldbb2
Class class	b — All beta proteins
Fold Fold fold	b.31 — EV matrix protein
Superfamily Superfamily superfamily	b.31.1 — EV matrix protein
Family Family family	b.31.1.1 — EV matrix protein

Domain ID domain_id	d4ldbc1
Class class	b — All beta proteins
Fold Fold fold	b.31 — EV matrix protein
Superfamily Superfamily superfamily	b.31.1 — EV matrix protein
Family Family family	b.31.1.1 — EV matrix protein

Domain ID domain_id	d4ldbd1
Class class	b — All beta proteins
Fold Fold fold	b.31 — EV matrix protein
Superfamily Superfamily superfamily	b.31.1 — EV matrix protein
Family Family family	b.31.1.1 — EV matrix protein

CATH v4.4 (8 domains)

Domain ID domain_id	4ldbA01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	20 — Topoisomerase I; domain 3
Homologous superfamily homologous superfamily	20 — Matrix protein VP40, N-terminal domain

Domain ID domain_id	4ldbA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	510 — EV matrix protein fold
Homologous superfamily homologous superfamily	10 — EV matrix protein

Domain ID domain_id	4ldbB01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	20 — Topoisomerase I; domain 3
Homologous superfamily homologous superfamily	20 — Matrix protein VP40, N-terminal domain

Domain ID domain_id	4ldbB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	510 — EV matrix protein fold
Homologous superfamily homologous superfamily	10 — EV matrix protein

Domain ID domain_id	4ldbC01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	20 — Topoisomerase I; domain 3
Homologous superfamily homologous superfamily	20 — Matrix protein VP40, N-terminal domain

Domain ID domain_id	4ldbC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	510 — EV matrix protein fold
Homologous superfamily homologous superfamily	10 — EV matrix protein

Domain ID domain_id	4ldbD01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	20 — Topoisomerase I; domain 3
Homologous superfamily homologous superfamily	20 — Matrix protein VP40, N-terminal domain

Domain ID domain_id	4ldbD02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	510 — EV matrix protein fold
Homologous superfamily homologous superfamily	10 — EV matrix protein

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Unit-cell length a length_a	160.005 Å
Unit-cell length b length_b	160.005 Å
Unit-cell length c length_c	89.745 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	24

Space group space_group	P 62
Space-group number int_tables_number	171
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2469
R_work r_work	0.2450
R_free r_free	0.2820

Description description	Matrix protein VP40
Molecular weight formula_weight	32244.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7574

Crystal Structure of Ebola Virus VP40 Dimer

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

Matrix protein VP40

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

4ldb__assembly_1__model_1

4ldb__assembly_1__model_1 | I(q)

4ldb__assembly_1__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	Ebola virus
Common name common_name	ZEBOV
NCBI taxonomy ID ncbi_taxonomy_id	186538
Host organism host_organism	Escherichia coli

Crystal Structure of Ebola Virus VP40 Dimer

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

Matrix protein VP40

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

4ldb__assembly_1__model_1

4ldb__assembly_1__model_1 | I(q)

4ldb__assembly_1__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)