› 4oiq

X-ray diffraction
3.62Å resolution

Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077 and rifampicin

Released:
DOI: 10.2210/pdb4oiq/pdb
PDB entry 4oiq coloured by chain, front view.
PDB entry 4oiq coloured by chain, side view.
PDB entry 4oiq coloured by chain, top view.
Source organisms:
Primary publication:
GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.
Zhang Y, Degen D, Ho MX, Sineva E, Ebright KY, Ebright YW, Mekler V, Vahedian-Movahed H, Feng Y, Yin R, Tuske S, Irschik H, Jansen R, Maffioli S, Donadio S, Arnold E, Ebright RH
Elife 3 e02450 (2014)
PMID: 24755292

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-238523 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
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:
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 HB8
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: 50.77 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:
Structure domains:
GE23077 Chain: I
Molecule details ›
Chain: I
Length: 7 amino acids
Theoretical weight: 740 Da
Source organism: Actinomadura sp.
Expression system: Not provided
5'-D(*CP*CP*T*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
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

Ligands and Environments

3 bound ligands:
Ligand ZN 2 x ZN
Ligand MG 4 x MG
Ligand MB8 1 x MB8
5 modified residues:
Ligand 2RA 1 x 2RA
Ligand DSN 1 x DSN
Ligand DVA 1 x DVA
Ligand 2TL 1 x 2TL
Ligand FGL 1 x FGL

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: C2
Unit cell:
a: 184.84Å b: 104.183Å c: 295.319Å
α: 90° β: 98.52° γ: 90°
R-values:
R R work R free
0.201 0.199 0.248
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

12 review citations

Structural biology of bacterial RNA polymerase.
Murakami KS. (2015)
11 more

1 mention without citation

GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.
Zhang et al. (2014)