SAXSdb — 2i8b

▼

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

Minor nucleoprotein VP30

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 142–272 Chain B； UniProt 142–272	Fragment：C-terminal domain, residues 142-272 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M ammonium acetate, 15mM magnesium acetate tetrahydrate, 0.05M sodium cacodylate, 10%(v/v) isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.241

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 2I8B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5DVW Structure of minor nucleoprotein V30 from Zaire ebolavirus Deposited 2015-09-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 142–272（131 aa） Fragment：UNP residues 142-272 Chain B 142–272（131 aa） Fragment：UNP residues 142-272	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；Molecular Dimensions Morpheus screen e12: 40mM each Di-Ethyleneglycol, Tri-Ethyleneglycol, TetraEthyleneglycol, Penta-Ethyleneglycol; 12.% each MPD, PEG 1000; PEG 3350; 100mM Tris(base)/Bicine pH 8.5; EbzaA.17250.a.EW11.PD00370 at 22 mg/ml, tray 262514e12, puck otj5-3; cryo: direct	Resolution 1.75 Å R-free 0.208
5DVW Structure of minor nucleoprotein V30 from Zaire ebolavirus Deposited 2015-09-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 142–272（131 aa） Fragment：UNP residues 142-272 Chain D 142–272（131 aa） Fragment：UNP residues 142-272	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；Molecular Dimensions Morpheus screen e12: 40mM each Di-Ethyleneglycol, Tri-Ethyleneglycol, TetraEthyleneglycol, Penta-Ethyleneglycol; 12.% each MPD, PEG 1000; PEG 3350; 100mM Tris(base)/Bicine pH 8.5; EbzaA.17250.a.EW11.PD00370 at 22 mg/ml, tray 262514e12, puck otj5-3; cryo: direct	Resolution 1.75 Å R-free 0.208
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 139–288（150 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288 Chain B 139–288（150 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 139–288（150 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288 Chain D 139–288（150 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 139–288（150 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288 Chain F 139–288（150 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 139–288（150 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288 Chain H 139–288（150 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 139–288（150 aa） Fragment：UNP P18272 residues 600-627,UNP Q05323 residues 139-288 Chain J 139–288（150 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

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

View Construct and Data Evidence

UniProt name	VP30_EBOZM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–152； UniProt 142–272 Author chain B； PDBConstruct 22–152； UniProt 142–272

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2i8b
Deposition date deposition_date	2006-09-01
Structure title title	Crystal structure of the C-terminal domain of Ebola virus VP30
Keywords keywords	VP30 Ebola virus protein, transcription, RNA binding, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.18 Å
Radius of gyration Rg (electron density) rg_electron	19.92 Å
Forward intensity I(0) i0	15073800.00
Molecular weight molecular_weight	29411.0 kDa
Excluded volume excluded_volume	36985 Å³
Envelope volume envelope_volume	44686 Å³
Hydration-shell volume shell_volume	19155 Å³
Envelope diameter envelope_diameter	67.0 Å
Shell Rg shell_rg	25.87 Å
Envelope Rg envelope_rg	20.18 Å
Shape Rg shape_rg	19.96 Å
Total Rg total_rg	20.68 Å
Total atoms total_atoms	2054
Residues n_residues	255
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	70.1 Å
Rg (real space) rg_real	21.17 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	1.5070e+07
I(0) uncertainty (real space) i0_real_error	2.0800e+05
Rg (reciprocal space) rg_reciprocal	21.17 Å
I(0) (reciprocal space) i0_reciprocal	15070000.0000
Solution quality estimate total_estimate	0.8014
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.7 Å
Skewness Skewness skewness	0.341
Kurtosis Kurtosis kurtosis	-0.418
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6510000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2i8bA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1160 —

Domain ID domain_id	2i8bB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1160 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	58.370 Å
Unit-cell length b length_b	63.590 Å
Unit-cell length c length_c	80.430 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.1974
R_work r_work	0.1950
R_free r_free	0.2406

Description description	Minor nucleoprotein VP30
Molecular weight formula_weight	17535.6 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	2253

Crystal structure of the C-terminal domain of Ebola virus VP30

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

Minor nucleoprotein VP30

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) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Zaire ebolavirus
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	174

fit	/app/data/saxs_computation/i8/2i8b/2i8b.fit
pddf	/app/data/pr_computation/i8/2i8b/2i8b.pr.out
profile	/app/data/saxs_computation/i8/2i8b/2i8b.dat