› 7mki

Electron Microscopy
3.5Å resolution

Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR (-5G to C) promoter DNA

Released:
DOI: 10.2210/pdb7mki/pdb
PDB entry 7mki coloured by chain, front view.
PDB entry 7mki coloured by chain, side view.
PDB entry 7mki coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Structural origins of Escherichia coli RNA polymerase open promoter complex stability.
Saecker RM, Chen J, Chiu CE, Malone B, Sotiris J, Ebrahim M, Yen LY, Eng ET, Darst SA
Proc Natl Acad Sci U S A 118 (2021)
PMID: 34599106
Related structures: EMD-23895

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 octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121642 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
DNA-directed RNA polymerase subunit alpha Chains: G, H
Molecule details ›
Chains: G, H
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A7Z4 (Residues: 1-329; Coverage: 100%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: I
Molecule details ›
Chain: I
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: J
Molecule details ›
Chain: J
Length: 1407 amino acids
Theoretical weight: 155.37 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A8T7 (Residues: 1-1407; Coverage: 100%)
Gene names: JW3951, b3988, rpoC, tabB
Sequence domains:
DNA-directed RNA polymerase subunit omega Chain: K
Molecule details ›
Chain: K
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A800 (Residues: 1-91; Coverage: 100%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor RpoD Chain: L
Molecule details ›
Chain: L
Length: 613 amino acids
Theoretical weight: 70.35 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Sequence domains:
Nontemplate strand of lambda PR DNA promoter (-5G to C) Chain: P
Molecule details ›
Chain: P
Length: 90 nucleotides
Theoretical weight: 27.84 KDa
Template strand of lambda PR promoter DNA (-5C to G) Chain: Q
Molecule details ›
Chain: Q
Length: 90 nucleotides
Theoretical weight: 27.67 KDa

Ligands and Environments

3 bound ligands:
Ligand 1N7 3 x 1N7
Ligand MG 1 x MG
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-23895
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Diverse molecular mechanisms of transcription regulation by the bacterial alarmone ppGpp.
Travis et al. (2022)
1 more