› 6ty9

Electron Microscopy
2.9Å resolution

In situ structure of BmCPV RNA dependent RNA polymerase at initiation state

Released:
DOI: 10.2210/pdb6ty9/pdb
PDB entry 6ty9 coloured by chain, front view.
PDB entry 6ty9 coloured by chain, side view.
PDB entry 6ty9 coloured by chain, top view.
Source organism: Bombyx mori cypovirus 1
Primary publication:
Conservative transcription in three steps visualized in a double-stranded RNA virus.
Cui Y, Zhang Y, Zhou K, Sun J, Zhou ZH
Nat Struct Mol Biol 26 1023-1034 (2019)
PMID: 31695188
Related structures: EMD-20582

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189189 (preferred)
Entry contents:
2 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (5 distinct):
RNA-directed RNA polymerase Chain: A
Molecule details ›
Chain: A
Length: 1225 amino acids
Theoretical weight: 139.01 KDa
Source organism: Bombyx mori cypovirus 1
UniProt:
  • Canonical: Q993A4 (Residues: 1-1225; Coverage: 100%)
Sequence domains:
Viral structural protein 4 Chain: B
Molecule details ›
Chain: B
Length: 561 amino acids
Theoretical weight: 63.68 KDa
Source organism: Bombyx mori cypovirus 1
UniProt:
  • Canonical: Q9IR43 (Residues: 1-561; Coverage: 100%)
Transcript Chain: M
Molecule details ›
Chain: M
Length: 2 nucleotides
Theoretical weight: 789 Da
Non-template RNA (5'-D(*(GTA))-R(P*GP*UP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3') Chain: N
Molecule details ›
Chain: N
Length: 19 nucleotides
Theoretical weight: 6.32 KDa
Template RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*UP*UP*AP*CP*U)-3') Chain: T
Molecule details ›
Chain: T
Length: 19 nucleotides
Theoretical weight: 6.12 KDa

Ligands and Environments

1 bound ligand:
Ligand MG 3 x MG
1 modified residue:
Ligand GTP 1 x GTP

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-20582

Quick links

Citations

1 review citation

RNA-dependent RNA polymerase (RdRp) inhibitors: The current landscape and repurposing for the COVID-19 pandemic.
Tian et al. (2021)
20 other articles

3 mentions without citation

Revisiting Viral RNA-Dependent RNA Polymerases: Insights from Recent Structural Studies.
Ramaswamy et al. (2022)
2 more