4aex

HCV-JFH1 NS5B POLYMERASE STRUCTURE AT 2.4 ANGSTROM in a primitive orthorhombic space group

Method: X-RAY DIFFRACTION Dmax: 115.4 Å Quality: REASONABLE

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

RNA-DIRECTED RNA POLYMERASE

HEPATITIS C VIRUS

UniProt Q99IB8

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 2442–3013 Fragment:CATALYTIC DOMAIN, RESIDUES 2442-3013 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;0.2 M SODIUM PHOSPHATE PH 6.5, 8-12% PEG 3350 Resolution 2.41 Å R-free 0.230
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 2442–3013 Fragment:CATALYTIC DOMAIN, RESIDUES 2442-3013 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;0.2 M SODIUM PHOSPHATE PH 6.5, 8-12% PEG 3350 Resolution 2.41 Å R-free 0.230

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.

31 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_HCVJF
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–573; UniProt 2442–3013 Author chain B; PDBConstruct 2–573; UniProt 2442–3013

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 4aex

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4aex
Deposition date deposition_date2012-01-12
Structure title titleHCV-JFH1 NS5B POLYMERASE STRUCTURE AT 2.4 ANGSTROM in a primitive orthorhombic space group
Keywords keywordsTRANSFERASE, HEPACIVIRUS, NONSTRUCTURAL PROTEINS, REPLICATION, DE NOVO INITIATION, PRIMING; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.76
Radius of gyration Rg (electron density) rg_electron34.95
Forward intensity I(0) i0242194000.00
Molecular weight molecular_weight125400.0 kDa
Excluded volume excluded_volume157060 ų
Envelope volume envelope_volume201640 ų
Hydration-shell volume shell_volume47438 ų
Envelope diameter envelope_diameter116.0
Shell Rg shell_rg42.16
Envelope Rg envelope_rg34.38
Shape Rg shape_rg34.93
Total Rg total_rg35.54
Total atoms total_atoms8804
Residues n_residues1127
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 dmax115.4
Rg (real space) rg_real35.74
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real2.4220e+08
I(0) uncertainty (real space) i0_real_error4.2660e+06
Rg (reciprocal space) rg_reciprocal35.76
I(0) (reciprocal space) i0_reciprocal242200000.0000
Solution quality estimate total_estimate0.6932
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.3
Skewness Skewness skewness0.268
Kurtosis Kurtosis kurtosis-0.597
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha43530000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 0.992; Smooth: 0.935

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4aexa_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.4 — RNA-dependent RNA-polymerase
Domain ID domain_idd4aexb_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.4 — RNA-dependent RNA-polymerase

8. Citations (1)

9. Files and Curves (10)