› 6oy7

X-ray diffraction
3.04Å resolution

X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter at 7 min

Released:
DOI: 10.2210/pdb6oy7/pdb
PDB entry 6oy7 coloured by chain, front view.
PDB entry 6oy7 coloured by chain, side view.
PDB entry 6oy7 coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase.
Shin Y, Hedglin M, Murakami KS
Nucleic Acids Res 48 2144-2155 (2020)
PMID: 31965171

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-215658 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (8 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
UniProt:
  • Canonical: Q5SHR6 (Residues: 1-315; Coverage: 100%)
Gene names: TTHA1664, rpoA
Sequence 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
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
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
UniProt:
  • Canonical: Q8RQE7 (Residues: 1-99; Coverage: 100%)
Gene names: TTHA1561, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor SigA Chain: F
Molecule details ›
Chain: F
Length: 423 amino acids
Theoretical weight: 48.6 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q5SKW1 (Residues: 1-423; Coverage: 100%)
Gene names: TTHA0532, sigA
Sequence domains:
DNA (5'-D(P*CP*CP*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*A)-3') Chain: G
Molecule details ›
Chain: G
Length: 22 nucleotides
Theoretical weight: 6.67 KDa
DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*TP*CP*TP*GP*AP*TP*GP*CP*AP*GP*G)-3') Chain: H
Molecule details ›
Chain: H
Length: 27 nucleotides
Theoretical weight: 8.41 KDa
RNA (5'-D(*(GTP))-R(P*GP*GP*GP*GP*G)-3') Chain: I
Molecule details ›
Chain: I
Length: 6 nucleotides
Theoretical weight: 2.19 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand POP 1 x POP
Ligand ZN 2 x ZN
1 modified residue:
Ligand GTP 1 x GTP

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: C2
Unit cell:
a: 185.684Å b: 101.609Å c: 295.796Å
α: 90° β: 98.76° γ: 90°
R-values:
R R work R free
0.208 0.207 0.248

Quick links

Citations

1 review citation

A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century.
Bremer et al. (2023)
4 other articles

2 mentions without citation

Watching the bacterial RNA polymerase transcription reaction by time-dependent soak-trigger-freeze X-ray crystallography.
Shin et al. (2021)
1 more