› 6n61

X-ray diffraction
3.25Å resolution

Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Capistruin

Released:
DOI: 10.2210/pdb6n61/pdb
PDB entry 6n61 coloured by chain, front view.
PDB entry 6n61 coloured by chain, side view.
PDB entry 6n61 coloured by chain, top view.
Source organisms:
Primary publication:
Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin.
Braffman NR, Piscotta FJ, Hauver J, Campbell EA, Link AJ, Darst SA
Proc Natl Acad Sci U S A 116 1273-1278 (2019)
PMID: 30626643

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-120317 (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: 239 amino acids
Theoretical weight: 26.46 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A7Z4 (Residues: 1-234; Coverage: 71%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains:
Structure domains:
DNA-directed RNA polymerase subunit beta Chain: C
Molecule details ›
Chain: C
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
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' Chain: D
Molecule details ›
Chain: D
Length: 1409 amino acids
Theoretical weight: 155.58 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A8T7 (Residues: 2-1407; Coverage: 100%)
Gene names: JW3951, b3988, rpoC, tabB
Sequence domains:
DNA-directed RNA polymerase subunit omega Chain: E
Molecule details ›
Chain: E
Length: 90 amino acids
Theoretical weight: 10.09 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A800 (Residues: 1-90; Coverage: 99%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
RNA polymerase sigma factor RpoD Chain: F
Molecule details ›
Chain: F
Length: 613 amino acids
Theoretical weight: 70.35 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q0P6L9 (Residues: 1-613; Coverage: 100%)
Gene name: rpoD
Sequence domains:
Capistruin Chain: I
Molecule details ›
Chain: I
Length: 19 amino acids
Theoretical weight: 2.07 KDa
Source organism: Burkholderia thailandensis E264
Expression system: Escherichia coli
non-template strand DNA Chain: N
Molecule details ›
Chain: N
Length: 29 nucleotides
Theoretical weight: 8.92 KDa
template strand DNA Chain: T
Molecule details ›
Chain: T
Length: 24 nucleotides
Theoretical weight: 7.36 KDa

Ligands and Environments

4 bound ligands:
Ligand EDO 1 x EDO
Ligand MG 1 x MG
Ligand ZN 2 x ZN
Ligand EPE 1 x EPE
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P41212
Unit cell:
a: 172.888Å b: 172.888Å c: 385.015Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.274 0.273 0.316
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

Quick links

Citations

20 review citations

New developments in RiPP discovery, enzymology and engineering.
Montalbán-López et al. (2021)
19 more

4 mentions without citation

Mechanisms of action of ribosomally synthesized and posttranslationally modified peptides (RiPPs).
Cao et al. (2021)
3 more