› 6kqd

X-ray diffraction
3.3Å resolution

Thermus thermophilus initial transcription complex comprising sigma A and 5'-OH RNA of 3 nt

Released:
DOI: 10.2210/pdb6kqd/pdb
PDB entry 6kqd coloured by chain, front view.
PDB entry 6kqd coloured by chain, side view.
PDB entry 6kqd 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-120167 (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, K, L
Molecule details ›
Chains: A, B, K, L
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 Chains: C, M
Molecule details ›
Chains: C, M
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' Chains: D, N
Molecule details ›
Chains: D, N
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 Chains: E, O
Molecule details ›
Chains: E, O
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 Chains: F, P
Molecule details ›
Chains: F, P
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*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*GP*G)-3') Chains: G, Q
Molecule details ›
Chains: G, Q
Length: 21 nucleotides
Theoretical weight: 6.44 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') Chains: H, R
Molecule details ›
Chains: H, R
Length: 27 nucleotides
Theoretical weight: 8.42 KDa
RNA (5'-R(*GP*GP*A)-3') Chains: I, S
Molecule details ›
Chains: I, S
Length: 3 nucleotides
Theoretical weight: 975 Da

Ligands and Environments

3 bound ligands:
Ligand MG 7 x MG
Ligand ZN 4 x ZN
Ligand DG 2 x DG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 185.501Å b: 104.044Å c: 297.441Å
α: 90° β: 98.5° γ: 90°
R-values:
R R work R free
0.207 0.207 0.25
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)