› 3cdw

X-ray diffraction
2.5Å resolution

Crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase (3Dpol) in complex with protein primer VPg and a pyrophosphate

Released:
DOI: 10.2210/pdb3cdw/pdb
PDB entry 3cdw coloured by chain, front view.
PDB entry 3cdw coloured by chain, side view.
PDB entry 3cdw coloured by chain, top view.
Source organism: Coxsackievirus B3 (strain Nancy)
Primary publication:
The crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase in complex with its protein primer VPg confirms the existence of a second VPg binding site on Picornaviridae polymerases.
Gruez A, Selisko B, Roberts M, Bricogne G, Bussetta C, Jabafi I, Coutard B, De Palma AM, Neyts J, Canard B
J Virol 82 9577-90 (2008)
PMID: 18632861

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Selective cleavage of Gln-|-Gly bond in the poliovirus polyprotein. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
Selective cleavage of Tyr-|-Gly bond in picornavirus polyprotein.
NTP + H(2)O = NDP + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-136768 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
RNA-directed RNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 468 amino acids
Theoretical weight: 53.28 KDa
Source organism: Coxsackievirus B3 (strain Nancy)
Expression system: Escherichia coli
UniProt:
  • Canonical: P03313 (Residues: 1724-2185; Coverage: 21%)
Sequence domains: Viral RNA-dependent RNA polymerase
Structure domains:
Viral protein genome-linked Chain: H
Molecule details ›
Chain: H
Length: 22 amino acids
Theoretical weight: 2.41 KDa
Source organism: Coxsackievirus B3 (strain Nancy)
Expression system: Not provided
UniProt:
  • Canonical: P03313 (Residues: 1519-1540; Coverage: 1%)

Ligands and Environments

4 bound ligands:
Ligand CL 7 x CL
Ligand ACT 6 x ACT
Ligand POP 1 x POP
Ligand GOL 27 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-3
Spacegroup: P43212
Unit cell:
a: 74.213Å b: 74.213Å c: 285.591Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.175 0.22
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

19 review citations

RNA Dependent RNA Polymerases: Insights from Structure, Function and Evolution.
Venkataraman et al. (2018)
18 more

11 mentions without citation

Picornaviral polymerase structure, function, and fidelity modulation.
Peersen OB. (2017)
10 more