› 5i2d

X-ray diffraction
4.4Å resolution

Crystal structure of T. thermophilus TTHB099 class II transcription activation complex: TAP-RPo

Released:
DOI: 10.2210/pdb5i2d/pdb
PDB entry 5i2d coloured by chain, front view.
PDB entry 5i2d coloured by chain, side view.
PDB entry 5i2d coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Structural basis of transcription activation.
Feng Y, Zhang Y, Ebright RH
Science 352 1330-3 (2016)
PMID: 27284196

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 undecamer (preferred)
PDBe Complex ID:
PDB-CPX-118770 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (9 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B, L, M
Molecule details ›
Chains: A, B, L, M
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, N
Molecule details ›
Chains: C, N
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, O
Molecule details ›
Chains: D, O
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, P
Molecule details ›
Chains: E, P
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, Q
Molecule details ›
Chains: F, Q
Length: 443 amino acids
Theoretical weight: 50.77 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5SKW1 (Residues: 1-423; Coverage: 100%)
Gene names: TTHA0532, sigA
Sequence domains:
Transcriptional regulator LdrP Chains: G, H, R, S
Molecule details ›
Chains: G, H, R, S
Length: 215 amino acids
Theoretical weight: 24.34 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli
UniProt:
  • Canonical: Q53W63 (Residues: 1-195; Coverage: 100%)
Gene name: TTHB099
Sequence domains:
DNA (72-MER) Chains: I, T
Molecule details ›
Chains: I, T
Length: 72 nucleotides
Theoretical weight: 22.23 KDa
DNA (72-MER) Chains: J, U
Molecule details ›
Chains: J, U
Length: 72 nucleotides
Theoretical weight: 22.34 KDa
RNA (5'-R(*UP*CP*GP*A)-3') Chains: K, V
Molecule details ›
Chains: K, V
Length: 4 nucleotides
Theoretical weight: 1.24 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P21
Unit cell:
a: 171.487Å b: 105.446Å c: 374.585Å
α: 90° β: 102.39° γ: 90°
R-values:
R R work R free
0.242 0.241 0.284
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Local and global regulation of transcription initiation in bacteria.
Browning et al. (2016)
13 more

11 mentions without citation

Early Evolution of Transcription Systems and Divergence of Archaea and Bacteria.
Lei et al. (2021)
10 more