› 4a8k

X-ray diffraction
3.5Å 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/pdb4a8k/pdb
PDB entry 4a8k coloured by chain, front view.
PDB entry 4a8k coloured by chain, side view.
PDB entry 4a8k 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

Assemblies composition:
monomeric
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117199 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 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(*AP*AP*TP*CP)-3' Chain: E
Molecule details ›
Chain: E
Length: 4 nucleotides
Theoretical weight: 1.17 KDa
Source organism: synthetic construct
Expression system: Not provided
5'-D(*TP*CP)-3' Chain: F
Molecule details ›
Chain: F
Length: 2 nucleotides
Theoretical weight: 548 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 106.53Å b: 93.028Å c: 140.86Å
α: 90° β: 101.36° γ: 90°
R-values:
R R work R free
0.278 0.276 0.307
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Common and unique features of viral RNA-dependent polymerases.
te Velthuis AJ. (2014)
2 more

3 mentions without citation

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