› 5x21

X-ray diffraction
3.32Å resolution

Crystal structure of Thermus thermophilus transcription initiation complex with GpA and pseudouridimycin (PUM)

Released:
DOI: 10.2210/pdb5x21/pdb
PDB entry 5x21 coloured by chain, front view.
PDB entry 5x21 coloured by chain, side view.
PDB entry 5x21 coloured by chain, top view.
Source organisms:
Primary publication:
Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase.
Maffioli SI, Zhang Y, Degen D, Carzaniga T, Del Gatto G, Serina S, Monciardini P, Mazzetti C, Guglierame P, Candiani G, Chiriac AI, Facchetti G, Kaltofen P, Sahl HG, Dehò G, Donadio S, Ebright RH
Cell 169 1240-1248.e23 (2017)
PMID: 28622509

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-215651 (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
Expression system: Thermus thermophilus
UniProt:
  • Canonical: Q5SHR6 (Residues: 1-315; Coverage: 100%)
Gene names: TTHA1664, 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 HB27
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: 443 amino acids
Theoretical weight: 50.74 KDa
Source organism: Thermus thermophilus HB27
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SKW1 (Residues: 1-423; Coverage: 100%)
Gene names: TTHA0532, sigA
Sequence domains:
promoter DNA template strand Chain: G
Molecule details ›
Chain: G
Length: 21 nucleotides
Theoretical weight: 6.46 KDa
promoter DNA nontemplate strand Chain: H
Molecule details ›
Chain: H
Length: 27 nucleotides
Theoretical weight: 8.42 KDa
RNA (5'-R(*GP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 2 nucleotides
Theoretical weight: 629 Da

Ligands and Environments

3 bound ligands:
Ligand MG 6 x MG
Ligand ZN 2 x ZN
Ligand PUM 1 x PUM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: C2
Unit cell:
a: 186.79Å b: 103.09Å c: 296.23Å
α: 90° β: 98.71° γ: 90°
R-values:
R R work R free
0.233 0.232 0.28
Expression systems:
  • Thermus thermophilus
  • Escherichia coli BL21(DE3)

Quick links

Citations

19 review citations

The evolution of nucleoside analogue antivirals: A review for chemists and non-chemists. Part 1: Early structural modifications to the nucleoside scaffold.
Seley-Radtke et al. (2018)
18 more

2 mentions without citation

Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3).
Lin et al. (2018)
1 more