1a6c

STRUCTURE OF TOBACCO RINGSPOT VIRUS

Method: X-RAY DIFFRACTION Dmax: 96.1 Å Quality: GOOD

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

TOBACCO RINGSPOT VIRUS CAPSID PROTEIN

OrganismNot specified

UniProt Q88894

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 × 60 PDB declaration: complete icosahedral assembly(60) Consistent with protein copy count Chain A; UniProt 3–515 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;VIRUS WAS CRYSTALLIZED USING HANGING DROP SETTING FROM RESERVOIR BUFFER CONTAINING 2-3% (W/V) PEG 3350, 1MM SODIUM AZIDE AND 0.125 M POTASSIUM PHOSPHATE, PH 6.5, pH 6.0, vapor diffusion - hanging drop Resolution 3.50 Å
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 3–515 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;VIRUS WAS CRYSTALLIZED USING HANGING DROP SETTING FROM RESERVOIR BUFFER CONTAINING 2-3% (W/V) PEG 3350, 1MM SODIUM AZIDE AND 0.125 M POTASSIUM PHOSPHATE, PH 6.5, pH 6.0, vapor diffusion - hanging drop Resolution 3.50 Å
3 Protein homooligomer Homooligomer Protein × 5 PDB declaration: pentameric(5) Consistent with protein copy count Chain A; UniProt 3–515 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;VIRUS WAS CRYSTALLIZED USING HANGING DROP SETTING FROM RESERVOIR BUFFER CONTAINING 2-3% (W/V) PEG 3350, 1MM SODIUM AZIDE AND 0.125 M POTASSIUM PHOSPHATE, PH 6.5, pH 6.0, vapor diffusion - hanging drop Resolution 3.50 Å
4 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 3–515 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;VIRUS WAS CRYSTALLIZED USING HANGING DROP SETTING FROM RESERVOIR BUFFER CONTAINING 2-3% (W/V) PEG 3350, 1MM SODIUM AZIDE AND 0.125 M POTASSIUM PHOSPHATE, PH 6.5, pH 6.0, vapor diffusion - hanging drop Resolution 3.50 Å
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 3–515 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;VIRUS WAS CRYSTALLIZED USING HANGING DROP SETTING FROM RESERVOIR BUFFER CONTAINING 2-3% (W/V) PEG 3350, 1MM SODIUM AZIDE AND 0.125 M POTASSIUM PHOSPHATE, PH 6.5, pH 6.0, vapor diffusion - hanging drop Resolution 3.50 Å
6 Protein homooligomer Homooligomer Protein × 30 PDB declaration: 30-meric(30) Consistent with protein copy count Chain A; UniProt 3–515 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;VIRUS WAS CRYSTALLIZED USING HANGING DROP SETTING FROM RESERVOIR BUFFER CONTAINING 2-3% (W/V) PEG 3350, 1MM SODIUM AZIDE AND 0.125 M POTASSIUM PHOSPHATE, PH 6.5, pH 6.0, vapor diffusion - hanging drop Resolution 3.50 Å

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 COAT_TRSV
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–513; UniProt 3–515

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 1a6c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1a6c
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1a6c
Deposition date deposition_date1998-02-23
Structure title titleSTRUCTURE OF TOBACCO RINGSPOT VIRUS
Keywords keywordsTRSV, NEPOVIRUS, VIRUS STRUCTURE, VIRUS EVOLUTION, PICORNAVIRUS SUPERFAMILY, VIRUS CAPSID PROTEIN, Icosahedral virus, Virus; VIRUS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.39
Radius of gyration Rg (electron density) rg_electron26.81
Forward intensity I(0) i052289600.00
Molecular weight molecular_weight56932.0 kDa
Excluded volume excluded_volume71396 ų
Envelope volume envelope_volume87811 ų
Hydration-shell volume shell_volume28224 ų
Envelope diameter envelope_diameter104.1
Shell Rg shell_rg33.05
Envelope Rg envelope_rg27.24
Shape Rg shape_rg26.78
Total Rg total_rg27.57
Total atoms total_atoms4016
Residues n_residues513
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax96.1
Rg (real space) rg_real27.46
Rg uncertainty (real space) rg_real_error0.92
I(0) (real space) i0_real5.2290e+07
I(0) uncertainty (real space) i0_real_error8.2860e+05
Rg (reciprocal space) rg_reciprocal27.44
I(0) (reciprocal space) i0_reciprocal52290000.0000
Solution quality estimate total_estimate0.7934
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary29.8
Skewness Skewness skewness0.389
Kurtosis Kurtosis kurtosis-0.357
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12120000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1a6ca1
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.2 — Comoviridae-like VP
Domain ID domain_idd1a6ca2
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.2 — Comoviridae-like VP
Domain ID domain_idd1a6ca3
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.2 — Comoviridae-like VP

CATH v4.4 (2 domains)

Domain ID domain_id1a6cA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id1a6cA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20

8. Citations (6)

9. Files and Curves (10)