› 6ca0

Electron Microscopy
5.75Å resolution

Cryo-EM structure of E. coli RNAP sigma70 open complex

Released:
DOI: 10.2210/pdb6ca0/pdb
PDB entry 6ca0 coloured by chain, front view.
PDB entry 6ca0 coloured by chain, side view.
PDB entry 6ca0 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Cryo-EM structure of Escherichia coli σ70 RNA polymerase and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation.
Narayanan A, Vago FS, Li K, Qayyum MZ, Yernool D, Jiang W, Murakami KS
J Biol Chem 293 7367-7375 (2018)
PMID: 29581236
Related structures: EMD-7439

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 decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119656 (preferred)
Entry contents:
5 distinct polypeptide molecules
4 distinct DNA molecules
Macromolecules (9 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B
Molecule details ›
Chains: A, B
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli K-12
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 Chain: C
Molecule details ›
Chain: C
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli K-12
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' Chain: D
Molecule details ›
Chain: D
Length: 1407 amino acids
Theoretical weight: 155.37 KDa
Source organism: Escherichia coli K-12
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 Chain: E
Molecule details ›
Chain: E
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Escherichia coli K-12
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 Chain: F
Molecule details ›
Chain: F
Length: 613 amino acids
Theoretical weight: 70.35 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Sequence domains:
DNA (45-MER) Chain: G
Molecule details ›
Chain: G
Length: 45 nucleotides
Theoretical weight: 13.87 KDa
DNA (35-MER) Chain: H
Molecule details ›
Chain: H
Length: 35 nucleotides
Theoretical weight: 10.79 KDa
DNA (5'-D(P*TP*CP*TP*GP*AP*CP*GP*CP*GP*GP*C)-3') Chain: I
Molecule details ›
Chain: I
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
DNA (5'-D(P*GP*CP*CP*GP*CP*GP*TP*CP*AP*GP*A)-3') Chain: J
Molecule details ›
Chain: J
Length: 11 nucleotides
Theoretical weight: 3.36 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 5.75Å
Relevant EMDB volumes: EMD-7439
Expression system: Escherichia coli

Quick links

Citations

3 review citations

The σ Subunit-Remodeling Factors: An Emerging Paradigms of Transcription Regulation.
Vishwakarma et al. (2020)
2 more

22 mentions without citation

Cryo-EM structure of Escherichia coli σ70 RNA polymerase and promoter DNA complex revealed a role of σ non-conserved region during the open complex formation.
Narayanan et al. (2018)
21 more