› 5voi

X-ray diffraction
2.8Å resolution

X-ray crystal structure of bacterial RNA polymerase and pyrG promoter complex

Released:
DOI: 10.2210/pdb5voi/pdb
PDB entry 5voi coloured by chain, front view.
PDB entry 5voi coloured by chain, side view.
PDB entry 5voi coloured by chain, top view.
Source organisms:
Primary publication:
X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway.
Murakami KS, Shin Y, Turnbough CL, Molodtsov V
Proc Natl Acad Sci U S A 114 8211-8216 (2017)
PMID: 28652344

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 octamer (preferred)
PDBe Complex ID:
PDB-CPX-215650 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B
Molecule details ›
Chains: A, B
Length: 315 amino acids
Theoretical weight: 35.06 KDa
Source organism: Thermus thermophilus HB27
UniProt:
  • Canonical: Q5SHR6 (Residues: 1-315; Coverage: 100%)
Gene names: TTHA1664, rpoA
Sequence domains:
Structure domains:
DNA-directed RNA polymerase subunit beta Chain: C
Molecule details ›
Chain: C
Length: 1119 amino acids
Theoretical weight: 125.44 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q8RQE9 (Residues: 1-1119; Coverage: 100%)
Gene names: TTHA1813, rpoB
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chain: D
Molecule details ›
Chain: D
Length: 1524 amino acids
Theoretical weight: 171 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q8RQE8 (Residues: 1-1524; Coverage: 100%)
Gene names: TTHA1812, rpoC
Sequence domains:
DNA-directed RNA polymerase subunit omega Chain: E
Molecule details ›
Chain: E
Length: 99 amino acids
Theoretical weight: 11.53 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q8RQE7 (Residues: 1-99; Coverage: 100%)
Gene names: TTHA1561, rpoZ
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
RNA polymerase sigma factor SigA Chain: F
Molecule details ›
Chain: F
Length: 423 amino acids
Theoretical weight: 48.6 KDa
Source organism: Thermus thermophilus HB8
UniProt:
  • Canonical: Q5SKW1 (Residues: 1-423; Coverage: 100%)
Gene names: TTHA0532, sigA
Sequence domains:
PyrG promoter Chain: G
Molecule details ›
Chain: G
Length: 22 nucleotides
Theoretical weight: 6.67 KDa
PyrG promoter Chain: H
Molecule details ›
Chain: H
Length: 27 nucleotides
Theoretical weight: 8.41 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: C2
Unit cell:
a: 183.18Å b: 103.474Å c: 294.444Å
α: 90° β: 99.14° γ: 90°
R-values:
R R work R free
0.193 0.192 0.236

Quick links

Citations

2 review citations

The Mechanisms of Substrate Selection, Catalysis, and Translocation by the Elongating RNA Polymerase.
Belogurov et al. (2019)
1 more

3 mentions without citation

The elemental mechanism of transcriptional pausing.
Saba et al. (2019)
2 more