› 4a8y

X-ray diffraction
3.41Å resolution

Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation

Released:
DOI: 10.2210/pdb4a8y/pdb
PDB entry 4a8y coloured by chain, front view.
PDB entry 4a8y coloured by chain, side view.
PDB entry 4a8y coloured by chain, top view.
Source organisms:
Primary publication:
Noncatalytic ions direct the RNA-dependent RNA polymerase of bacterial double-stranded RNA virus ϕ6 from de novo initiation to elongation.
Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes JM
J Virol 86 2837-49 (2012)
PMID: 22205747

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117204 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
RNA-directed RNA polymerase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 665 amino acids
Theoretical weight: 75.03 KDa
Source organism: Pseudomonas virus phi6
Expression system: Escherichia coli
UniProt:
  • Canonical: P11124 (Residues: 1-665; Coverage: 100%)
Gene name: P2
Sequence domains: Viral RNA-dependent RNA polymerase
Structure domains:
5'-D(*TP*TP*TP*TP*CP*GP*CP*GP*TP*AP*AP*GP*CP*GP)-3' Chains: F, G, H
Molecule details ›
Chains: F, G, H
Length: 14 nucleotides
Theoretical weight: 4.29 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 2 x MG
Ligand ATP 3 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P21
Unit cell:
a: 105.76Å b: 89.29Å c: 140.99Å
α: 90° β: 101.88° γ: 90°
R-values:
R R work R free
0.22 0.218 0.255
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

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

2 mentions without citation

Cystoviral RNA-directed RNA polymerases: Regulation of RNA synthesis on multiple time and length scales.
Alphonse et al. (2017)
1 more