SAXSdb — 2og3

▼

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

Nucleocapsid protein

SARS coronavirus Tor2

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 49–174	Fragment：rna binding domain of N protein	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；277 K；40% MPD and 0.1 M Tris pH 8.0, typically crystals appear within 2 weeks, VAPOR DIFFUSION, temperature 277K	Resolution 1.85 Å R-free 0.247

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 2OG3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1SSK Structure of the N-terminal RNA-binding Domain of the SARS CoV Nucleocapsid Protein Deposited 2004-03-24	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 45–181（137 aa） Fragment：N-terminal Domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 100mM Nacl；Pressure ambient NMR sample composition 0.5 mM N-terminal SARS CoV NP, U-15N,90% H2O/10% 2H2O, 50 mM sodium phosphate (pH 6.8) and 100 mM sodium chloride.	Resolution not provided
1X7Q Crystal structure of HLA-A*1101 with sars nucleocapsid peptide Deposited 2004-08-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 362–370（9 aa）	Not recorded	SO4 SULFATE ION × 3 GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.15 K；25% PEG 5000 MME, 0.2M AMMONIUM SULFATE, 0.1M MES PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.45 Å R-free 0.181
2CJR Crystal structure of oligomerization domain of SARS coronavirus nucleocapsid protein. Deposited 2006-04-06	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 248–365（118 aa） Fragment：RESIDUES 248-365 Chain B 248–365（118 aa） Fragment：RESIDUES 248-365	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 2.50 Å R-free 0.269
2CJR Crystal structure of oligomerization domain of SARS coronavirus nucleocapsid protein. Deposited 2006-04-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 248–365（118 aa） Fragment：RESIDUES 248-365 Chain D 248–365（118 aa） Fragment：RESIDUES 248-365	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 2.50 Å R-free 0.269
2CJR Crystal structure of oligomerization domain of SARS coronavirus nucleocapsid protein. Deposited 2006-04-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 248–365（118 aa） Fragment：RESIDUES 248-365 Chain F 248–365（118 aa） Fragment：RESIDUES 248-365	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 2.50 Å R-free 0.269
2CJR Crystal structure of oligomerization domain of SARS coronavirus nucleocapsid protein. Deposited 2006-04-06	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 248–365（118 aa） Fragment：RESIDUES 248-365 Chain H 248–365（118 aa） Fragment：RESIDUES 248-365	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.00	Resolution 2.50 Å R-free 0.269
2GIB Crystal structure of the SARS coronavirus nucleocapsid protein dimerization domain Deposited 2006-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 270–370（101 aa） Fragment：dimerization domain (residues 270-370) Chain B 270–370（101 aa） Fragment：dimerization domain (residues 270-370)	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.5 K；30-33% Pentaerythritol ethoxylate 15/4 EO/OH, 50 mM Ammonium sulfate, 50 mM Bis-Tris , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.5K	Resolution 1.75 Å R-free 0.235
2GIB Crystal structure of the SARS coronavirus nucleocapsid protein dimerization domain Deposited 2006-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 270–370（101 aa） Fragment：dimerization domain (residues 270-370) Chain B 270–370（101 aa） Fragment：dimerization domain (residues 270-370)	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.5 K；30-33% Pentaerythritol ethoxylate 15/4 EO/OH, 50 mM Ammonium sulfate, 50 mM Bis-Tris , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.5K	Resolution 1.75 Å R-free 0.235
2GIB Crystal structure of the SARS coronavirus nucleocapsid protein dimerization domain Deposited 2006-03-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 270–370（101 aa） Fragment：dimerization domain (residues 270-370) Chain B 270–370（101 aa） Fragment：dimerization domain (residues 270-370)	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277.5 K；30-33% Pentaerythritol ethoxylate 15/4 EO/OH, 50 mM Ammonium sulfate, 50 mM Bis-Tris , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.5K	Resolution 1.75 Å R-free 0.235
2JW8 Solution structure of stereo-array isotope labelled (SAIL) C-terminal dimerization domain of SARS coronavirus nucleocapsid protein Deposited 2007-10-06	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 248–365（118 aa） Fragment：UNP residues 248-365 Chain B 248–365（118 aa） Fragment：UNP residues 248-365	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) 50；Pressure AMBIENT NMR sample composition 0.5mM SAIL-C-terminal dimerization domain of SARS coronavirus nucleocapsid protein, 10mM sodium phosphate, 50mM NaCl, 1mM EDTA, 1mM DSS, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2OFZ Ultrahigh Resolution Crystal Structure of RNA Binding Domain of SARS Nucleopcapsid (N Protein) at 1.1 Angstrom Resolution in Monoclinic Form. Deposited 2007-01-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 49–174（126 aa） Fragment：RNA BINDING DOMAIN OF SARS NUCLEOCAPSID	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；25% PEG 2000MME, 0.2 M sodium bromide, 0.1 M sodium acetate, bcip ADDITIVE, VAPOR DIFFUSION, SITTING DROP	Resolution 1.17 Å R-free 0.191
3I6L Newly identified epitope N1 derived from SARS-CoV N protein complexed with HLA-A*2402 Deposited 2009-07-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 346–354（9 aa） Fragment：UNP residue 346-354	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；277 K；0.2M Ammonium sulfate, 0.1M Tris pH 8.9, 25% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.40 Å R-free 0.284
7LG0 Human leukocyte antigen B*07:02 in complex with SARS-CoV2 epitope SPRWYFYYL Deposited 2021-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 106–114（9 aa） Fragment：UNP residues 105-113	Not recorded	P6G HEXAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；290 K；0.1 M HEPES-NaOH, pH 7.5, 2 M ammonium sulfate	Resolution 2.30 Å R-free 0.268

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

View Construct and Data Evidence

UniProt name	NCAP_CVHSA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–93； UniProt 49–174

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	2og3
Deposition date deposition_date	2007-01-05
Structure title title	structure of the rna binding domain of n protein from SARS coronavirus in cubic crystal form
Keywords keywords	n protein, nucleocapsid, rna binding domain, sars coronavirus, 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	14.71 Å
Radius of gyration Rg (electron density) rg_electron	13.24 Å
Forward intensity I(0) i0	3122250.00
Molecular weight molecular_weight	12281.0 kDa
Excluded volume excluded_volume	15352 Å³
Envelope volume envelope_volume	17516 Å³
Hydration-shell volume shell_volume	11287 Å³
Envelope diameter envelope_diameter	46.2 Å
Shell Rg shell_rg	18.86 Å
Envelope Rg envelope_rg	13.65 Å
Shape Rg shape_rg	13.19 Å
Total Rg total_rg	14.64 Å
Total atoms total_atoms	873
Residues n_residues	112
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	47.5 Å
Rg (real space) rg_real	14.61 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	3.1220e+06
I(0) uncertainty (real space) i0_real_error	3.5330e+04
Rg (reciprocal space) rg_reciprocal	14.61 Å
I(0) (reciprocal space) i0_reciprocal	3122000.0000
Solution quality estimate total_estimate	0.8849
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.2 Å
Skewness Skewness skewness	0.100
Kurtosis Kurtosis kurtosis	-0.396
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	708700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.977

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▶

8. Citations (1)

▶

Unit-cell length a length_a	110.001 Å
Unit-cell length b length_b	110.001 Å
Unit-cell length c length_c	110.001 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	24

Space group space_group	I 21 3
Space-group number int_tables_number	199
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	38.900 Å
R factor r_factor	0.2013
R_work r_work	0.1990
R_free r_free	0.2471

Description description	Nucleocapsid protein
Molecular weight formula_weight	15392.1 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	1132

structure of the rna binding domain of n protein from SARS coronavirus in cubic crystal form

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

Nucleocapsid protein

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	SARS coronavirus Tor2
NCBI Class编号 ncbi_taxonomy_id	227984
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	243

fit	/app/data/saxs_computation/og/2og3/2og3.fit
pddf	/app/data/pr_computation/og/2og3/2og3.pr.out
profile	/app/data/saxs_computation/og/2og3/2og3.dat