1d1d

NMR SOLUTION STRUCTURE OF THE CAPSID PROTEIN FROM ROUS SARCOMA VIRUS

Method: SOLUTION NMR Dmax: 95.4 Å Quality: REASONABLE

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

PROTEIN (CAPSID PROTEIN)

Rous sarcoma virus

UniProt O92954

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 240–479 Mutation:N-TERMINAL HIS-TAGGED No other associated polymer SOLUTION NMR NMR measurement conditions:pH 6;303 K;Ionic strength (raw mmCIF value) 10 mM PHOSPHATE;Pressure 1 NMR sample composition:~1 MM CA_RSV, 10 MM PHOSPHATE (PH 6.0), 0.2 MM N3NA, 0.1 MM EDTA, 0.1 MM PMSF, 1 MG/L PEPSTATIN A, 5 MM BETA-MERCAPTOETHANOL | 90% H2O/10% D2O NMR sample composition:~1 MM CA_RSV, 10 MM PHOSPHATE (PH 6.0), 0.2 MM N3NA, 0.1 MM EDTA, 0.1 MM PMSF, 1 MG/L PEPSTATIN A, 5 MM BETA-MERCAPTOETHANOL | 100% D2O Resolution not provided

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 O92954_RSVSB
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 23–262; UniProt 240–479

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 1d1d

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d1d
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d1d
Deposition date deposition_date1999-09-15
Structure title titleNMR SOLUTION STRUCTURE OF THE CAPSID PROTEIN FROM ROUS SARCOMA VIRUS
Keywords keywordsTWO INDEPENDENT DOMAINS HELICAL BUNDLES, VIRUS/VIRAL PROTEIN, Viral protein; VIRAL PROTEIN
Experimental Method methodSOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier36.27
Radius of gyration Rg (electron density) rg_electron36.37
Forward intensity I(0) i03128390000.00
Molecular weight molecular_weight475790.0 kDa
Excluded volume excluded_volume598960 ų
Envelope volume envelope_volume466790 ų
Hydration-shell volume shell_volume83612 ų
Envelope diameter envelope_diameter171.5
Shell Rg shell_rg51.10
Envelope Rg envelope_rg46.04
Shape Rg shape_rg36.40
Total Rg total_rg36.64
Total atoms total_atoms67900
Residues n_residues4400
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 dmax95.4
Rg (real space) rg_real34.01
Rg uncertainty (real space) rg_real_error0.20
I(0) (real space) i0_real2.9770e+09
I(0) uncertainty (real space) i0_real_error3.7740e+07
Rg (reciprocal space) rg_reciprocal36.40
I(0) (reciprocal space) i0_reciprocal3128000000.0000
Solution quality estimate total_estimate0.6847
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary36.9
Skewness Skewness skewness0.257
Kurtosis Kurtosis kurtosis-0.694
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha1.2590
Highest regularization parameter α highest_alpha22410000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.001; Oscil: 0.998; Stabil: 0.981; Sysdev: 0.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1d1da1
Class classa — All alpha proteins
Fold Fold folda.28 — Acyl carrier protein-like
Superfamily Superfamily superfamilya.28.3 — Retrovirus capsid dimerization domain-like
Family Family familya.28.3.1 — Retrovirus capsid protein C-terminal domain
Domain ID domain_idd1d1da2
Class classa — All alpha proteins
Fold Fold folda.73 — Retrovirus capsid protein, N-terminal core domain
Superfamily Superfamily superfamilya.73.1 — Retrovirus capsid protein, N-terminal core domain
Family Family familya.73.1.1 — Retrovirus capsid protein, N-terminal core domain

CATH v4.4 (2 domains)

Domain ID domain_id1d1dA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology375 — Human Immunodeficiency Virus Type 1 Capsid Protein
Homologous superfamily homologous superfamily10 — Human Immunodeficiency Virus Type 1 Capsid Protein
Domain ID domain_id1d1dA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1200 — Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
Homologous superfamily homologous superfamily30 — Retrovirus capsid C-terminal domain

8. Citations (1)

9. Files and Curves (10)