SAXSdb — 4m0q

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

Membrane-associated protein VP24

Zaire ebolavirus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 11–237 Chain B； UniProt 11–237	Fragment：UNP residues 11-231	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.4；298 K；150 mM MES, pH 6.4, 20% Jeffamine M-600, pH 7.0, 50 mM cesium chloride, 6 mM barium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.92 Å R-free 0.232

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 4M0Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4U2X Ebola virus VP24 in complex with Karyopherin alpha 5 C-terminus Deposited 2014-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 16–231（216 aa） Fragment：eVP24	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；3.5M ammonium chloride, 0.1 M Bis-Tris propane	Resolution 3.15 Å R-free 0.249
4U2X Ebola virus VP24 in complex with Karyopherin alpha 5 C-terminus Deposited 2014-07-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 16–231（216 aa） Fragment：eVP24	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；3.5M ammonium chloride, 0.1 M Bis-Tris propane	Resolution 3.15 Å R-free 0.249
4U2X Ebola virus VP24 in complex with Karyopherin alpha 5 C-terminus Deposited 2014-07-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 16–231（216 aa） Fragment：eVP24	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；3.5M ammonium chloride, 0.1 M Bis-Tris propane	Resolution 3.15 Å R-free 0.249
6EHM Model of the Ebola virus nucleocapsid subunit from recombinant virus-like particles Deposited 2017-09-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–251（251 aa） Chain D 1–251（251 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.30 Å
8USN Intracellular cryo-tomography structure of EBOV nucleocapsid at 8.9 Angstrom Deposited 2023-10-27	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain I 1–251（251 aa） Chain J 1–251（251 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 8.90 Å
8UST In-virion structure of Ebola virus nucleocapsid-like assemblies from recombinant virus-like particles (nucleoprotein, VP24,VP35,VP40) Deposited 2023-10-29	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 7 PDB declaration: nonameric	Chain I 1–251（251 aa） Chain J 1–251（251 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.30 Å
8Y9J Structure of the Ebola virus nucleocapsid subunit Deposited 2024-02-06	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric	Chain C 1–251（251 aa） Chain D 1–251（251 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；The sample was applied to both sides of the grid. The grids were blotted for 14 seconds.	Resolution 4.60 Å

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VP24_EBOZM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–230； UniProt 11–237 Author chain B； PDBConstruct 4–230； UniProt 11–237

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	4m0q
Deposition date deposition_date	2013-08-01
Structure title title	Ebola virus VP24 structure
Keywords keywords	Ebola virus virulence factor, VIRAL PROTEIN; VIRAL PROTEIN
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	26.96 Å
Radius of gyration Rg (electron density) rg_electron	25.93 Å
Forward intensity I(0) i0	38330800.00
Molecular weight molecular_weight	50133.0 kDa
Excluded volume excluded_volume	63728 Å³
Envelope volume envelope_volume	76580 Å³
Hydration-shell volume shell_volume	25727 Å³
Envelope diameter envelope_diameter	100.5 Å
Shell Rg shell_rg	31.85 Å
Envelope Rg envelope_rg	26.17 Å
Shape Rg shape_rg	25.91 Å
Total Rg total_rg	26.64 Å
Total atoms total_atoms	3528
Residues n_residues	444
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	94.8 Å
Rg (real space) rg_real	27.11 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	3.8330e+07
I(0) uncertainty (real space) i0_real_error	5.7040e+05
Rg (reciprocal space) rg_reciprocal	27.07 Å
I(0) (reciprocal space) i0_reciprocal	38330000.0000
Solution quality estimate total_estimate	0.8416
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.488
Kurtosis Kurtosis kurtosis	-0.250
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8733000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.724; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.771; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	71.775 Å
Unit-cell length b length_b	71.775 Å
Unit-cell length c length_c	191.165 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.921 Å
Low-resolution limit resolution_low	33.597 Å
R factor r_factor	0.2107
R_work r_work	0.2095
R_free r_free	0.2315

Description description	Membrane-associated protein VP24
Molecular weight formula_weight	25921.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3703

Ebola virus VP24 structure

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

Membrane-associated protein VP24

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Zaire ebolavirus
通用名 common_name	ZEBOV
NCBI Class编号 ncbi_taxonomy_id	186538
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	170

fit	/app/data/saxs_computation/m0/4m0q/4m0q.fit
pddf	/app/data/pr_computation/m0/4m0q/4m0q.pr.out
profile	/app/data/saxs_computation/m0/4m0q/4m0q.dat