› 6vjs

X-ray diffraction
4.02Å resolution

Escherichia coli RNA polymerase and ureidothiophene-2-carboxylic acid complex

Released:
DOI: 10.2210/pdb6vjs/pdb
PDB entry 6vjs coloured by chain, front view.
PDB entry 6vjs coloured by chain, side view.
PDB entry 6vjs coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Evaluation of Bacterial RNA Polymerase Inhibitors in a Staphylococcus aureus-Based Wound Infection Model in SKH1 Mice.
Haupenthal J, Kautz Y, Elgaher WAM, Pätzold L, Röhrig T, Laschke MW, Tschernig T, Hirsch AKH, Molodtsov V, Murakami KS, Hartmann RW, Bischoff M
ACS Infect Dis 6 2573-2581 (2020)
PMID: 32886885

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 hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132730 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B, F, G
Molecule details ›
Chains: A, B, F, G
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A7Z4 (Residues: 1-329; Coverage: 100%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains:
DNA-directed RNA polymerase subunit beta Chains: C, H
Molecule details ›
Chains: C, H
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8V2 (Residues: 1-1342; Coverage: 100%)
Gene names: JW3950, b3987, groN, nitB, rif, ron, rpoB, stl, stv, tabD
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chains: D, I
Molecule details ›
Chains: D, I
Length: 1407 amino acids
Theoretical weight: 155.37 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A8T7 (Residues: 1-1407; Coverage: 100%)
Gene names: JW3951, b3988, rpoC, tabB
Sequence domains:
DNA-directed RNA polymerase subunit omega Chains: E, J
Molecule details ›
Chains: E, J
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A800 (Residues: 1-91; Coverage: 100%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor RpoD Chains: X, Y
Molecule details ›
Chains: X, Y
Length: 613 amino acids
Theoretical weight: 70.35 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand QZY 1 x QZY
Ligand ZN 4 x ZN
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P212121
Unit cell:
a: 187.077Å b: 205.501Å c: 309.88Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.23 0.276
Expression system: Escherichia coli

Quick links

Citations

4 citation in other articles

IL-17C and IL-17RE Promote Wound Closure in a Staphylococcus aureus-Based Murine Wound Infection Model.
Pätzold et al. (2021)
3 more