SAXSdb — 4ldd

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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 6	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

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	4ldd
Deposition date deposition_date	2013-06-24
Structure title title	Crystal Structure of Ebola virus VP40 Hexamer
Keywords keywords	ebolavirus matrix assembly, 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.

4ldd__assembly_1__model_1

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

Download this curve (.dat)

4ldd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ldd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.38 Å
Rg (electron density)	42.21 Å
Total Rg	42.37 Å
Atom count	7766
Residues	1004
Excluded volume	140980 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ldd__assembly_1__model_1`	hexameric （6）	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) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4lddA00
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	4lddB01
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	4lddB02
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	4lddC00
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

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Unit-cell length a length_a	134.479 Å
Unit-cell length b length_b	134.479 Å
Unit-cell length c length_c	136.087 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	3.498 Å
Low-resolution limit resolution_low	44.885 Å
R factor r_factor	0.3071
R_work r_work	0.3063
R_free r_free	0.3225

Description description	Matrix protein VP40
Molecular weight formula_weight	32244.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,A
Atom count atom_count	3883

Crystal Structure of Ebola virus VP40 Hexamer

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

4ldd__assembly_1__model_1

4ldd__assembly_1__model_1 | I(q)

4ldd__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) 4 domains

CATH v4.4 (4 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 Hexamer

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

4ldd__assembly_1__model_1

4ldd__assembly_1__model_1 | I(q)

4ldd__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)