SAXSdb — 4u2x

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 16–231	Fragment：eVP24	Importin subunit alpha-6 × 1 （O15131） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 16–231	Fragment：eVP24	Importin subunit alpha-6 × 1 （O15131） 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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 16–231	Fragment：eVP24	Importin subunit alpha-6 × 1 （O15131）	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

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 4U2X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4M0Q Ebola virus VP24 structure Deposited 2013-08-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 11–237（227 aa） Fragment：UNP residues 11-231 Chain B 11–237（227 aa） Fragment：UNP residues 11-231	Not recorded	No recorded non-water small molecule	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
6EHM Model of the Ebola virus nucleocapsid subunit from recombinant virus-like particles Deposited 2017-09-13	Different construct Different mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 5 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 1–216； UniProt 16–231 Author chain B； PDBConstruct 1–216； UniProt 16–231 Author chain C； PDBConstruct 1–216； UniProt 16–231

Importin subunit alpha-6

Homo sapiens

UniProt O15131

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 329–503	Fragment：KPNA5	Membrane-associated protein VP24 × 1 （Q05322） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 329–503	Fragment：KPNA5	Membrane-associated protein VP24 × 1 （Q05322） 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
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain F； UniProt 329–503	Fragment：KPNA5	Membrane-associated protein VP24 × 1 （Q05322）	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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	IMA6_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–175； UniProt 329–503 Author chain E； PDBConstruct 1–175； UniProt 329–503 Author chain F； PDBConstruct 1–175； UniProt 329–503

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	4u2x
Deposition date deposition_date	2014-07-18
Structure title title	Ebola virus VP24 in complex with Karyopherin alpha 5 C-terminus
Keywords keywords	eVP24, importin alpha6, immune antagonist, 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	39.70 Å
Radius of gyration Rg (electron density) rg_electron	39.32 Å
Forward intensity I(0) i0	241007000.00
Molecular weight molecular_weight	130300.0 kDa
Excluded volume excluded_volume	165040 Å³
Envelope volume envelope_volume	225680 Å³
Hydration-shell volume shell_volume	48435 Å³
Envelope diameter envelope_diameter	134.3 Å
Shell Rg shell_rg	44.33 Å
Envelope Rg envelope_rg	38.45 Å
Shape Rg shape_rg	39.30 Å
Total Rg total_rg	39.69 Å
Total atoms total_atoms	9165
Residues n_residues	1162
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	126.2 Å
Rg (real space) rg_real	39.55 Å
Rg uncertainty (real space) rg_real_error	0.98 Å
I(0) (real space) i0_real	2.4100e+08
I(0) uncertainty (real space) i0_real_error	4.2420e+06
Rg (reciprocal space) rg_reciprocal	39.65 Å
I(0) (reciprocal space) i0_reciprocal	241000000.0000
Solution quality estimate total_estimate	0.9027
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	56.8 Å
Skewness Skewness skewness	0.106
Kurtosis Kurtosis kurtosis	-0.650
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38000000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.922

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Membrane-associated protein VP24
Molecular weight formula_weight	24421.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9199

DLEKGVVLSDLCNFLVSQTIQGWKVYWAGIEFDVTHKGMALLHRLKTNDFAPAWSMTRNLFPHLFQNPNSTIESPLWALRVILAAGIQDQLIDQSLIEPLAGALGLISDWLLTTNTNHFNMRTQRVKEQLSLKMLSLIRSNILKFINKLDALHVVNYNGLLSSIEIGTQNHTIIITRTNMGFLVELQEPDKSAMNRMKPGPAKFSLLHESTLKAFT

来源 Source

来源生物 organism	Zaire ebolavirus
通用名 common_name	ZEBOV
NCBI Class编号 ncbi_taxonomy_id	128952
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Importin subunit alpha-6
Molecular weight formula_weight	19477.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

TQVILNCSALPCLLHLLSSPKESIRKEACWTVSNITAGNRAQIQAVIDANIFPVLIEILQKAEFRTRKEAAWAITNATSGGTPEQIRYLVALGCIKPLCDLLTVMDSKIVQVALNGLENILRLGEQESKQNGIGINPYCALIEEAYGLDKIEFLQSHENQEIYQKAFDLIEHYFG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	24

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	4u2xD00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	4u2xE00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	4u2xF00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

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8. Citations (1)

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Unit-cell length a length_a	103.925 Å
Unit-cell length b length_b	103.925 Å
Unit-cell length c length_c	333.630 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	18

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	3.153 Å
Low-resolution limit resolution_low	35.120 Å
R factor r_factor	0.2163
R_work r_work	0.2146
R_free r_free	0.2492

fit	/app/data/saxs_computation/u2/4u2x/4u2x.fit
pddf	/app/data/pr_computation/u2/4u2x/4u2x.pr.out
profile	/app/data/saxs_computation/u2/4u2x/4u2x.dat

Ebola virus VP24 in complex with Karyopherin alpha 5 C-terminus

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

Importin subunit alpha-6

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)