SAXSdb — 7k5l

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

Matrix protein VP40

Zaire ebolavirus (strain Mayinga-76)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 8 RNA 8	HSP RNA oligonucleotide × 8 water × 16	Consistent with all polymers

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 16–166； UniProt 44–194

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	7k5l
Deposition date deposition_date	2020-09-17
Structure title title	Ebola virus VP40 octameric ring generated by an RNA oligonucleotide
Keywords keywords	Ebola virus, transformer protein, RNA binding protein, matrix protein, 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.

7k5l__assembly_1__model_1

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

Download this curve (.dat)

7k5l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7k5l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.02 Å
Rg (electron density)	31.83 Å
Total Rg	32.59 Å
Atom count	8120
Residues	1016
Excluded volume	145660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7k5l__assembly_1__model_1`	hexadecameric （16）	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	Matrix protein VP40
Molecular weight formula_weight	19117.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1148

MAHHHHHHVDDDDKMGDTPSNPLRPIADDTIDHASHTPGSVSSAFILEAMVNVISGPKVLMKQIPIWLPLGVADQKTYSFDSTTAAIMLASYTITHFGKATNPLVRVNRLGPGIPDHPLRLLRIGNQAFLQEFVLPPVQLPQYFTFDLTALKLITQPLPAATWTDDENLYFQ

Source Source

Source organism organism	Zaire ebolavirus (strain Mayinga-76)
Common name common_name	ZEBOV
NCBI taxonomy ID ncbi_taxonomy_id	128952
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	HSP RNA oligonucleotide
Molecular weight formula_weight	11056.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R

UACAUUCCCAGCCUUUGUAGUGUUUUCGCCAAGCA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	99

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Unit-cell length a length_a	80.626 Å
Unit-cell length b length_b	80.626 Å
Unit-cell length c length_c	47.083 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	8

Space group space_group	P 4 2 2
Space-group number int_tables_number	89
Crystal system crystal_system	tetragonal

Resolution resolution	1.380 Å
Low-resolution limit resolution_low	23.540 Å
R factor r_factor	0.1810
R_work r_work	0.1802
R_free r_free	0.1970

Ebola virus VP40 octameric ring generated by an RNA oligonucleotide

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

7k5l__assembly_1__model_1

7k5l__assembly_1__model_1 | I(q)

7k5l__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (1)

Ebola virus VP40 octameric ring generated by an RNA oligonucleotide

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

7k5l__assembly_1__model_1

7k5l__assembly_1__model_1 | I(q)

7k5l__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Citations (1)