› 4wtj

X-ray diffraction
2.2Å resolution

CRYSTAL STRUCTURE OF HCV NS5B GENOTYPE 2A JFH-1 ISOLATE WITH S15G E86Q E87Q C223H V321I MUTATIONS IN COMPLEX WITH RNA TEMPLATE 5'-AUCC, RNA PRIMER 5'-PGG, MN2+, AND ADP

Released:
DOI: 10.2210/pdb4wtj/pdb
PDB entry 4wtj coloured by chain, front view.
PDB entry 4wtj coloured by chain, side view.
PDB entry 4wtj coloured by chain, top view.
Source organisms:
Primary publication:
Viral replication. Structural basis for RNA replication by the hepatitis C virus polymerase.
Appleby TC, Perry JK, Murakami E, Barauskas O, Feng J, Cho A, Fox D, Wetmore DR, McGrath ME, Ray AS, Sofia MJ, Swaminathan S, Edwards TE
Science 347 771-5 (2015)
PMID: 25678663

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
NTP + H(2)O = NDP + phosphate
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189316 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
RNA-directed RNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 580 amino acids
Theoretical weight: 64.82 KDa
Source organism: Hepatitis C virus JFH-1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q99IB8 (Residues: 2443-3012; Coverage: 19%)
Sequence domains: Viral RNA dependent RNA polymerase
RNA TEMPLATE AUCC Chain: T
Molecule details ›
Chain: T
Length: 4 nucleotides
Theoretical weight: 1.2 KDa
Source organism: synthetic construct
Expression system: Not provided
RNA PRIMER GG Chain: P
Molecule details ›
Chain: P
Length: 2 nucleotides
Theoretical weight: 645 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

7 bound ligands:
Ligand MN 2 x MN
Ligand CL 1 x CL
Ligand ADP 1 x ADP
Ligand PG6 1 x PG6
Ligand B3P 1 x B3P
Ligand PG4 1 x PG4
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: P65
Unit cell:
a: 139.87Å b: 139.87Å c: 92.7Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.178 0.176 0.211
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

51 review citations

Coronavirus RNA Proofreading: Molecular Basis and Therapeutic Targeting.
Robson et al. (2020)
50 more

6 mentions without citation

A Structural Overview of RNA-Dependent RNA Polymerases from the Flaviviridae Family.
Wu et al. (2015)
5 more