› 6wox

X-ray diffraction
3.14Å resolution

Thermus thermophilus RNA polymerase initially transcribing complex with 2'dCTP

Released:
DOI: 10.2210/pdb6wox/pdb
PDB entry 6wox coloured by chain, front view.
PDB entry 6wox coloured by chain, side view.
PDB entry 6wox coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases.
Mäkinen JJ, Shin Y, Vieras E, Virta P, Metsä-Ketelä M, Murakami KS, Belogurov GA
Nat Commun 12 796 (2021)
PMID: 33542236

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-120855 (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: 1505 amino acids
Theoretical weight: 168.82 KDa
Source organism: Thermus thermophilus
UniProt:
  • Canonical: Q8RQE8 (Residues: 1-1505; Coverage: 99%)
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*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*GP*CP*AP*G)-3') Chain: G
Molecule details ›
Chain: G
Length: 22 nucleotides
Theoretical weight: 6.71 KDa
DNA (25-MER) Chain: H
Molecule details ›
Chain: H
Length: 27 nucleotides
Theoretical weight: 8.42 KDa
RNA (5'-R(*GP*CP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 3 nucleotides
Theoretical weight: 935 Da

Ligands and Environments

4 bound ligands:
Ligand NA 1 x NA
Ligand DCP 1 x DCP
Ligand MG 1 x MG
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: C2
Unit cell:
a: 185.435Å b: 102.654Å c: 295.382Å
α: 90° β: 98.914° γ: 90°
R-values:
R R work R free
0.197 0.196 0.261

Quick links

Citations

2 review citations

Dissecting nucleotide selectivity in viral RNA polymerases.
Long et al. (2021)
1 more

1 mention without citation

The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases.
Mäkinen et al. (2021)