› 6gh6

Electron Microscopy
4.1Å resolution

Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme intermediate partially loaded complex

Released:
DOI: 10.2210/pdb6gh6/pdb
PDB entry 6gh6 coloured by chain, front view.
PDB entry 6gh6 coloured by chain, side view.
PDB entry 6gh6 coloured by chain, top view.
Source organisms:
Primary publication:
Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation.
Glyde R, Ye F, Jovanovic M, Kotta-Loizou I, Buck M, Zhang X
Mol Cell 70 1111-1120.e3 (2018)
PMID: 29932903
Related structures: EMD-0002

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)
PDBe Complex ID:
PDB-CPX-119953 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 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 'BL21-Gold(DE3)pLysS AG'
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 'BL21-Gold(DE3)pLysS AG'
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 'BL21-Gold(DE3)pLysS AG'
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 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P0A800 (Residues: 1-91; Coverage: 100%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma-54 factor Chain: M
Molecule details ›
Chain: M
Length: 497 amino acids
Theoretical weight: 54.74 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P06223 (Residues: 1-477; Coverage: 100%)
Gene names: ntrA, rpoN
Sequence domains:
nifH promoter non-tmeplate DNA Chain: N
Molecule details ›
Chain: N
Length: 63 nucleotides
Theoretical weight: 19.49 KDa
nifH promoter template DNA Chain: T
Molecule details ›
Chain: T
Length: 63 nucleotides
Theoretical weight: 19.4 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-0002
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

3 review citations

Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms.
Mazumder et al. (2019)
2 more

5 mentions without citation

Mechanisms of σ54-Dependent Transcription Initiation and Regulation.
Danson et al. (2019)
4 more