SAXSdb — 4qb0

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

Nucleoprotein

Ebola virus

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 641–739	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；19.3% PEG3350, 0.05M Magnesium Formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.75 Å R-free 0.225

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 4QB0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4QAZ The crystal structure of the C-terminal domain of Ebola (Zaire) nucleoprotein Deposited 2014-05-06	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 641–739（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；19.3% PEG3350, 0.3M Magnesium Formate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.98 Å R-free 0.229
4YPI Structure of Ebola virus nucleoprotein N-terminal fragment bound to a peptide derived from Ebola VP35 Deposited 2015-03-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 38–385（348 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；streak seeding in well solution containing 100 mM Tris pH 7.2, 50 mM Hepes pH 7, and 23% PEG400	Resolution 3.71 Å R-free 0.285
4YPI Structure of Ebola virus nucleoprotein N-terminal fragment bound to a peptide derived from Ebola VP35 Deposited 2015-03-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 38–385（348 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；streak seeding in well solution containing 100 mM Tris pH 7.2, 50 mM Hepes pH 7, and 23% PEG400	Resolution 3.71 Å R-free 0.285
4YPI Structure of Ebola virus nucleoprotein N-terminal fragment bound to a peptide derived from Ebola VP35 Deposited 2015-03-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 38–385（348 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；streak seeding in well solution containing 100 mM Tris pH 7.2, 50 mM Hepes pH 7, and 23% PEG400	Resolution 3.71 Å R-free 0.285
4YPI Structure of Ebola virus nucleoprotein N-terminal fragment bound to a peptide derived from Ebola VP35 Deposited 2015-03-13	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 38–385（348 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；streak seeding in well solution containing 100 mM Tris pH 7.2, 50 mM Hepes pH 7, and 23% PEG400	Resolution 3.71 Å R-free 0.285
4Z9P Crystal structure of Ebola virus nucleoprotein core domain at 1.8A resolution Deposited 2015-04-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 36–351（316 aa） Fragment：core domain (UNP RESIDUES 36-351)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7；289 K；200mM ammonium citrate tribasic pH 7.0, 20% (w/v) PEG 3350	Resolution 1.79 Å R-free 0.225
4ZTA Ebola virus nucleoprotein bound to VP35 chaperoning peptide I212121 Deposited 2015-05-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–367（335 aa） Fragment：UNP Q05127 residues 15-59,UNP P18272 residues 33-367,UNP Q05127 residues 15-59,UNP P18272 residues 33-367	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；277 K；2.2M Sodium formate, 100mM NaOAc pH 4.7	Resolution 2.40 Å R-free 0.233
4ZTG Ebola virus nucleoprotein bound to VP35 chaperoning peptide P22121 Deposited 2015-05-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–367（335 aa） Fragment：UNP Q05127 residues 15-59, UNP P18272 residues 33-367	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；277 K；12% PEG 6000, 100 mM MES pH 5.0	Resolution 2.80 Å R-free 0.293
4ZTI Ebola virus nucleoprotein bound to VP35 chaperoning peptide P212121 Deposited 2015-05-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–367（335 aa） Fragment：UNP Q05127 residues 15-59,UNP P18272 residues 33-367	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.4；277 K；2.0 M sodium formate, 100 mM sodium acetate pH 4.4	Resolution 2.40 Å R-free 0.247
4ZTI Ebola virus nucleoprotein bound to VP35 chaperoning peptide P212121 Deposited 2015-05-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 33–367（335 aa） Fragment：UNP Q05127 residues 15-59,UNP P18272 residues 33-367	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.4；277 K；2.0 M sodium formate, 100 mM sodium acetate pH 4.4	Resolution 2.40 Å R-free 0.247
5T3T Ebola virus VP30 CTD bound to nucleoprotein Deposited 2016-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 600–627（28 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288 Chain B 600–627（28 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；298 K；0.3 uL of 20 mg/mL protein mixed with 0.3 uL of 2.2 M ammonium sulfate, 100 mM sodium acetate pH 4.9	Resolution 2.20 Å R-free 0.249
5T3T Ebola virus VP30 CTD bound to nucleoprotein Deposited 2016-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 600–627（28 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288 Chain D 600–627（28 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；298 K；0.3 uL of 20 mg/mL protein mixed with 0.3 uL of 2.2 M ammonium sulfate, 100 mM sodium acetate pH 4.9	Resolution 2.20 Å R-free 0.249
5T3T Ebola virus VP30 CTD bound to nucleoprotein Deposited 2016-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 600–627（28 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288 Chain F 600–627（28 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288	Not recorded	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；298 K；0.3 uL of 20 mg/mL protein mixed with 0.3 uL of 2.2 M ammonium sulfate, 100 mM sodium acetate pH 4.9	Resolution 2.20 Å R-free 0.249
5T3T Ebola virus VP30 CTD bound to nucleoprotein Deposited 2016-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 600–627（28 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288 Chain H 600–627（28 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；298 K；0.3 uL of 20 mg/mL protein mixed with 0.3 uL of 2.2 M ammonium sulfate, 100 mM sodium acetate pH 4.9	Resolution 2.20 Å R-free 0.249
5T3T Ebola virus VP30 CTD bound to nucleoprotein Deposited 2016-08-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain I 600–627（28 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288 Chain J 600–627（28 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.9；298 K；0.3 uL of 20 mg/mL protein mixed with 0.3 uL of 2.2 M ammonium sulfate, 100 mM sodium acetate pH 4.9	Resolution 2.20 Å R-free 0.249
6EHL Model of the Ebola virus nucleoprotein in recombinant nucleocapsid-like assemblies Deposited 2017-09-13	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–739（739 aa）	Mutation：Truncation mutant (residues 1-450)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
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 A 1–739（739 aa） Chain B 1–739（739 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
6NUT Ebola virus nucleoprotein - RNA complex Deposited 2019-02-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 50 PDB declaration: 100-meric	Chain A 1–450（450 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
6NUT Ebola virus nucleoprotein - RNA complex Deposited 2019-02-01	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–450（450 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 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 A 1–739（739 aa） Chain B 1–739（739 aa） Chain E 1–739（739 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 A 1–739（739 aa） Chain B 1–739（739 aa） Chain E 1–739（739 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 A 1–739（739 aa） Chain B 1–739（739 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

13 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NCAP_EBOZM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–103； UniProt 641–739

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	4qb0
Deposition date deposition_date	2014-05-06
Structure title title	The crystal structure of the C-terminal domain of Ebola (Zaire) nucleoprotein
Keywords keywords	new family, Ebola virus VP40, 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	15.64 Å
Radius of gyration Rg (electron density) rg_electron	14.50 Å
Forward intensity I(0) i0	2633900.00
Molecular weight molecular_weight	11207.0 kDa
Excluded volume excluded_volume	13904 Å³
Envelope volume envelope_volume	16055 Å³
Hydration-shell volume shell_volume	10116 Å³
Envelope diameter envelope_diameter	54.8 Å
Shell Rg shell_rg	19.09 Å
Envelope Rg envelope_rg	14.96 Å
Shape Rg shape_rg	14.43 Å
Total Rg total_rg	15.67 Å
Total atoms total_atoms	1495
Residues n_residues	95
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	53.6 Å
Rg (real space) rg_real	15.67 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	2.6340e+06
I(0) uncertainty (real space) i0_real_error	3.0720e+04
Rg (reciprocal space) rg_reciprocal	15.67 Å
I(0) (reciprocal space) i0_reciprocal	2634000.0000
Solution quality estimate total_estimate	0.7863
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	19.7 Å
Skewness Skewness skewness	0.424
Kurtosis Kurtosis kurtosis	-0.056
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	332000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.760; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.000

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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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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4qb0a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.399 — Ebola nucleoprotein C-terminal domain-like
Superfamily Superfamily superfamily	d.399.1 — Ebola nucleoprotein C-terminal domain-like
Family Family family	d.399.1.1 — Ebola nucleoprotein C-terminal domain-like

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8. Citations (1)

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Unit-cell length a length_a	36.599 Å
Unit-cell length b length_b	49.169 Å
Unit-cell length c length_c	53.806 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	29.359 Å
R factor r_factor	0.1850
R_work r_work	0.1830
R_free r_free	0.2249

Description description	Nucleoprotein
Molecular weight formula_weight	12339.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1617

The crystal structure of the C-terminal domain of Ebola (Zaire) nucleoprotein

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

Nucleoprotein

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

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Ebola virus
通用名 common_name	ZEBOV
NCBI Class编号 ncbi_taxonomy_id	128952
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	95

fit	/app/data/saxs_computation/qb/4qb0/4qb0.fit
pddf	/app/data/pr_computation/qb/4qb0/4qb0.pr.out
profile	/app/data/saxs_computation/qb/4qb0/4qb0.dat