› 3vnu

X-ray diffraction
3.2Å resolution

Complex structure of viral RNA polymerase I

Released:
DOI: 10.2210/pdb3vnu/pdb
PDB entry 3vnu coloured by chain, front view.
PDB entry 3vnu coloured by chain, side view.
PDB entry 3vnu coloured by chain, top view.
Source organisms:
Primary publication:
Mechanism for template-independent terminal adenylation activity of Qβ replicase.
Takeshita D, Yamashita S, Tomita K
Structure 20 1661-9 (2012)
PMID: 22884418

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-238697 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
Elongation factor Ts; Elongation factor Tu; RNA-directed RNA polymerase subunit beta Chain: A
Molecule details ›
Chain: A
Length: 1289 amino acids
Theoretical weight: 141.42 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: P0A6P3 (Residues: 1-283; Coverage: 100%)
  • Canonical: P0A6N3 (Residues: 1-394; Coverage: 100%)
  • Canonical: P14647 (Residues: 1-589; Coverage: 100%)
Gene names: ECs0172, ECs4190, ECs4903, Z0181, Z4697, Z5553, tsf, tufA, tufB
Sequence domains:
Structure domains:
RNA (5'-R(*CP*CP*CP*UP*AP*CP*CP*C)-3') Chain: G
Molecule details ›
Chain: G
Length: 8 nucleotides
Theoretical weight: 2.42 KDa
RNA (5'-R(*GP*GP*GP*UP*AP*GP*GP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 8 nucleotides
Theoretical weight: 2.66 KDa

Ligands and Environments

2 bound ligands:
Ligand ATP 1 x ATP
Ligand CA 2 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: C2221
Unit cell:
a: 139.005Å b: 255.506Å c: 101.425Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.276 0.274 0.316
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Structures and functions of Qβ replicase: translation factors beyond protein synthesis.
Tomita K. (2014)
1 more

1 mention without citation

Structural Insights into the Binding Modes of Viral RNA-Dependent RNA Polymerases Using a Function-Site Interaction Fingerprint Method for RNA Virus Drug Discovery.
Zhao et al. (2020)