› 8que

Electron Microscopy
3.3Å resolution

Structure of the Bacteriophage PhiKZ non-virion RNA Polymerase bound to DNA and RNA

Released:
DOI: 10.2210/pdb8que/pdb
PDB entry 8que coloured by chain, front view.
PDB entry 8que coloured by chain, side view.
PDB entry 8que coloured by chain, top view.
Source organism: Pseudomonas phage phiKZ
Primary publication:
Structure of the Bacteriophage PhiKZ non-virion RNA Polymerase transcribing from its promoter p119L.
de Martín Garrido N, Chen CS, Ramlaul K, Aylett CHS, Yakunina M
J Mol Biol 168713 (2024)
PMID: 39029888
Related structures: EMD-18661

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-247599 (preferred)
Entry contents:
5 distinct polypeptide molecules
3 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (9 distinct):
DNA-directed RNA polymerase; PHIKZ056.1 Chain: A
Molecule details ›
Chain: A
Length: 508 amino acids
Theoretical weight: 57.98 KDa
Source organism: Pseudomonas phage phiKZ
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8SDA7 (Residues: 1-419; Coverage: 100%)
  • Canonical: L7T138 (Residues: 1-61; Coverage: 100%)
DNA-directed RNA polymerase; PHIKZ071 Chain: C
Molecule details ›
Chain: C
Length: 700 amino acids
Theoretical weight: 78.78 KDa
Source organism: Pseudomonas phage phiKZ
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8SD91 (Residues: 1-393; Coverage: 100%)
  • Canonical: Q8SD89 (Residues: 1-295; Coverage: 100%)
PHIKZ074 Chain: D
Molecule details ›
Chain: D
Length: 677 amino acids
Theoretical weight: 77.51 KDa
Source organism: Pseudomonas phage phiKZ
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8SD88 (Residues: 1-677; Coverage: 100%)
PHIKZ123 Chain: E
Molecule details ›
Chain: E
Length: 543 amino acids
Theoretical weight: 62.96 KDa
Source organism: Pseudomonas phage phiKZ
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8SD39 (Residues: 1-543; Coverage: 100%)
PHIKZ068 Chain: B
Molecule details ›
Chain: B
Length: 521 amino acids
Theoretical weight: 59.42 KDa
Source organism: Pseudomonas phage phiKZ
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8SD94 (Residues: 1-521; Coverage: 100%)
DNA Chain: F
Molecule details ›
Chain: F
Length: 75 nucleotides
Theoretical weight: 23.1 KDa
DNA Chain: G
Molecule details ›
Chain: G
Length: 75 nucleotides
Theoretical weight: 23.06 KDa
DNA Chains: I, J
Molecule details ›
Chains: I, J
Length: 17 nucleotides
Theoretical weight: 3.02 KDa
RNA Chain: H
Molecule details ›
Chain: H
Length: 8 nucleotides
Theoretical weight: 2.59 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-18661
Expression system: Escherichia coli BL21(DE3)

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