› 7s01

X-ray diffraction
3.4Å resolution

X-ray structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with a forked oligonucleotide containing the P077 promoter

Released:
DOI: 10.2210/pdb7s01/pdb
PDB entry 7s01 coloured by chain, front view.
PDB entry 7s01 coloured by chain, side view.
PDB entry 7s01 coloured by chain, top view.
Source organism: Bacillus phage AR9
Primary publication:
Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase.
Fraser A, Sokolova ML, Drobysheva AV, Gordeeva JV, Borukhov S, Jumper J, Severinov KV, Leiman PG
Nat Commun 13 3526 (2022)
PMID: 35725571

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 nonamer (preferred)
PDBe Complex ID:
PDB-CPX-103098 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
DNA-directed RNA polymerase subunit Chain: A
Molecule details ›
Chain: A
Length: 464 amino acids
Theoretical weight: 54.92 KDa
Source organism: Bacillus phage AR9
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A172JIC8 (Residues: 1-464; Coverage: 100%)
Gene name: AR9_g226
DNA-directed RNA polymerase Chain: d
Molecule details ›
Chain: d
Length: 426 amino acids
Theoretical weight: 49.4 KDa
Source organism: Bacillus phage AR9
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A172JIH0 (Residues: 1-426; Coverage: 100%)
Gene name: AR9_g270
DNA-directed RNA polymerase beta subunit Chain: c
Molecule details ›
Chain: c
Length: 496 amino acids
Theoretical weight: 58.11 KDa
Source organism: Bacillus phage AR9
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A172JI16 (Residues: 1-496; Coverage: 100%)
Gene name: AR9_g105
DNA-directed RNA polymerase Chain: D
Molecule details ›
Chain: D
Length: 631 amino acids
Theoretical weight: 73.1 KDa
Source organism: Bacillus phage AR9
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A172JI62 (Residues: 1-631; Coverage: 100%)
Gene name: AR9_g154
Sequence domains: RNA polymerase Rpb1, domain 5
DNA-directed RNA polymerase Chain: C
Molecule details ›
Chain: C
Length: 665 amino acids
Theoretical weight: 76.98 KDa
Source organism: Bacillus phage AR9
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A172JHZ2 (Residues: 1-665; Coverage: 100%)
Gene name: AR9_g089
Sequence domains: RNA polymerase Rpb2, domain 6
Non-template strand of the forked DNA oligonucleotide (downstream copy) Chains: N, t
Molecule details ›
Chains: N, t
Length: 14 nucleotides
Theoretical weight: 4.3 KDa
Template strand of the forked DNA oligonucleotide (downstream copy) containing the P077 AR9 promoter motif Chains: T, n
Molecule details ›
Chains: T, n
Length: 32 nucleotides
Theoretical weight: 9.76 KDa

Ligands and Environments

5 bound ligands:
Ligand UMP 5 x UMP
Ligand DG 1 x DG
Ligand ZN 1 x ZN
Ligand DT 1 x DT
Ligand DA 1 x DA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: C2
Unit cell:
a: 176.925Å b: 110.455Å c: 222.379Å
α: 90° β: 98.517° γ: 90°
R-values:
R R work R free
0.242 0.239 0.293
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

Tail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail.
Chaban et al. (2024)