› 4yfn

X-ray diffraction
3.82Å resolution

Escherichia coli RNA polymerase in complex with squaramide compound 14 (N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide)

Released:
DOI: 10.2210/pdb4yfn/pdb
PDB entry 4yfn coloured by chain, front view.
PDB entry 4yfn coloured by chain, side view.
PDB entry 4yfn coloured by chain, top view.
Source organisms:
Primary publication:
X-ray crystal structures of Escherichia coli RNA polymerase with switch region binding inhibitors enable rational design of squaramides with an improved fraction unbound to human plasma protein.
Molodtsov V, Fleming PR, Eyermann CJ, Ferguson AD, Foulk MA, McKinney DC, Masse CE, Buurman ET, Murakami KS
J Med Chem 58 3156-71 (2015)
PMID: 25798859

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)
PDBe Complex ID:
PDB-CPX-108535 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B, G, H
Molecule details ›
Chains: A, B, G, H
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli O139:H28 str. E24377A
Expression system: Escherichia coli #1/H766
UniProt:
  • Canonical: A7ZSI4 (Residues: 1-329; Coverage: 100%)
Gene names: EcE24377A_3778, rpoA
Sequence domains:
Structure domains:
DNA-directed RNA polymerase subunit beta Chains: C, I
Molecule details ›
Chains: C, I
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli O139:H28 str. E24377A
Expression system: Escherichia coli #1/H766
UniProt:
  • Canonical: A7ZUK1 (Residues: 1-1342; Coverage: 100%)
Gene names: EcE24377A_4528, rpoB
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chains: D, J
Molecule details ›
Chains: D, J
Length: 1407 amino acids
Theoretical weight: 155.37 KDa
Source organism: Escherichia coli O139:H28 str. E24377A
Expression system: Escherichia coli #1/H766
UniProt:
  • Canonical: A7ZUK2 (Residues: 1-1407; Coverage: 100%)
Gene names: EcE24377A_4529, rpoC
Sequence domains:
DNA-directed RNA polymerase subunit omega Chains: E, K
Molecule details ›
Chains: E, K
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Escherichia coli O139:H28 str. E24377A
Expression system: Escherichia coli #1/H766
UniProt:
  • Canonical: A7ZTK1 (Residues: 1-91; Coverage: 100%)
Gene names: EcE24377A_4152, rpoZ
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
RNA polymerase sigma factor RpoD Chains: F, L
Molecule details ›
Chains: F, L
Length: 613 amino acids
Theoretical weight: 70.35 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli #1/H766
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand MG 2 x MG
Ligand ZN 4 x ZN
Ligand 4C2 2 x 4C2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P212121
Unit cell:
a: 191.247Å b: 206.569Å c: 312.146Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.222 0.27
Expression system: Escherichia coli #1/H766

Quick links

Citations

5 review citations

Bacterial Transcription as a Target for Antibacterial Drug Development.
Ma et al. (2016)
4 more

3 mentions without citation

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