› 4q5s

X-ray diffraction
3Å resolution

Thermus thermophilus RNA polymerase initially transcribing complex containing 6-mer RNA

Released:
DOI: 10.2210/pdb4q5s/pdb
PDB entry 4q5s coloured by chain, front view.
PDB entry 4q5s coloured by chain, side view.
PDB entry 4q5s coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme.
Basu RS, Warner BA, Molodtsov V, Pupov D, Esyunina D, Fernández-Tornero C, Kulbachinskiy A, Murakami KS
J Biol Chem 289 24549-59 (2014)
PMID: 24973216

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-118007 (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: Q9Z9H6 (Residues: 1-315; Coverage: 100%)
Gene name: 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
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SKW1 (Residues: 1-423; Coverage: 100%)
Gene names: TTHA0532, sigA
Sequence domains:
Structure domains:
DNA (5'-D(*CP*CP*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*GP*CP*AP*GP*CP*CP*A)-3') Chain: G
Molecule details ›
Chain: G
Length: 22 nucleotides
Theoretical weight: 6.71 KDa
DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3') Chain: H
Molecule details ›
Chain: H
Length: 27 nucleotides
Theoretical weight: 8.42 KDa
RNA (5'-R(P*CP*UP*CP*AP*C)-3') Chain: I
Molecule details ›
Chain: I
Length: 5 nucleotides
Theoretical weight: 1.51 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand ZN 2 x ZN
Ligand ATP 1 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: C2
Unit cell:
a: 187.089Å b: 102.075Å c: 297.263Å
α: 90° β: 98.14° γ: 90°
R-values:
R R work R free
0.27 0.269 0.294
Expression system: Escherichia coli

Quick links

Citations

21 review citations

Initial events in bacterial transcription initiation.
Ruff et al. (2015)
20 more

5 mentions without citation

Structural biology of bacterial RNA polymerase.
Murakami KS. (2015)
4 more