› 6kqn

X-ray diffraction
3.49Å resolution

Thermus thermophilus initial transcription complex comprising sigma A and 5'-triphosphate RNA of 6 nt

Released:
DOI: 10.2210/pdb6kqn/pdb
PDB entry 6kqn coloured by chain, front view.
PDB entry 6kqn coloured by chain, side view.
PDB entry 6kqn coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y
Proc Natl Acad Sci U S A 117 5801-5809 (2020)
PMID: 32127479

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-120174 (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 HB8
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 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
RNA polymerase sigma factor SigA Chain: F
Molecule details ›
Chain: F
Length: 443 amino acids
Theoretical weight: 50.77 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SKW1 (Residues: 1-423; Coverage: 100%)
Gene names: TTHA0532, sigA
Sequence domains:
DNA (5'-D(*CP*CP*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3') Chain: G
Molecule details ›
Chain: G
Length: 21 nucleotides
Theoretical weight: 6.48 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(*(CTP))-R(P*CP*UP*CP*GP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 6 nucleotides
Theoretical weight: 2.01 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 4 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: 184.621Å b: 101.92Å c: 296.11Å
α: 90° β: 98.83° γ: 90°
R-values:
R R work R free
0.216 0.213 0.258
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Diverse and unified mechanisms of transcription initiation in bacteria.
Chen et al. (2021)
2 more

1 mention without citation

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Li et al. (2020)