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4z9p

Crystal structure of Ebola virus nucleoprotein core domain at 1.8A resolution

Method: X-RAY DIFFRACTION Dmax: 74.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Nucleoprotein

Zaire ebolavirus (strain Mayinga-76)

UniProt P18272

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 36–351 Fragment：core domain (UNP RESIDUES 36-351) No other associated polymer 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

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 4Z9P 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 construct 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
4QB0 The crystal structure of the C-terminal domain of Ebola (Zaire) nucleoprotein Deposited 2014-05-06 Different construct 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, 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
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
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 2–317； UniProt 36–351

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4z9p

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4z9p
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4z9p
Deposition date deposition_date2015-04-11
Structure title titleCrystal structure of Ebola virus nucleoprotein core domain at 1.8A resolution
Keywords keywordsEbola, Filoviridae, nucleoprotein, RNA binding protein, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.44 Å
Radius of gyration Rg (electron density) rg_electron21.50 Å
Forward intensity I(0) i017612800.00
Molecular weight molecular_weight32642.0 kDa
Excluded volume excluded_volume41330 ų
Envelope volume envelope_volume49588 ų
Hydration-shell volume shell_volume20203 ų
Envelope diameter envelope_diameter74.8 Å
Shell Rg shell_rg27.27 Å
Envelope Rg envelope_rg21.73 Å
Shape Rg shape_rg21.47 Å
Total Rg total_rg22.41 Å
Total atoms total_atoms2301
Residues n_residues293
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax74.5 Å
Rg (real space) rg_real22.49 Å
Rg uncertainty (real space) rg_real_error0.59 Å
I(0) (real space) i0_real1.7610e+07
I(0) uncertainty (real space) i0_real_error2.2490e+05
Rg (reciprocal space) rg_reciprocal22.48 Å
I(0) (reciprocal space) i0_reciprocal17610000.0000
Solution quality estimate total_estimate0.8776
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.9 Å
Skewness Skewness skewness0.449
Kurtosis Kurtosis kurtosis-0.178
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4920000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.830; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.943
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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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9. Files and Curves (10)