› 5nss

Electron Microscopy
5.8Å resolution

Cryo-EM structure of RNA polymerase-sigma54 holoenzyme with promoter DNA and transcription activator PspF intermedate complex

Released:
DOI: 10.2210/pdb5nss/pdb
PDB entry 5nss coloured by chain, front view.
PDB entry 5nss coloured by chain, side view.
PDB entry 5nss coloured by chain, top view.
Source organisms:
Primary publication:
Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.
Glyde R, Ye F, Darbari VC, Zhang N, Buck M, Zhang X
Mol Cell 67 106-116.e4 (2017)
PMID: 28579332
Related structures: EMD-3696

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 tetradecamer (preferred)
PDBe Complex ID:
PDB-CPX-119072 (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: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli K-12
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: 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(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: 1449 amino acids
Theoretical weight: 158.94 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A8T7 (Residues: 1-98, 99-1407; 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(DE3)
UniProt:
  • Canonical: P0A800 (Residues: 1-91; Coverage: 100%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
Psp operon transcriptional activator Chains: F, G, J, K, L, N
Molecule details ›
Chains: F, G, J, K, L, N
Length: 295 amino acids
Theoretical weight: 33.19 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P37344 (Residues: 1-275; Coverage: 85%)
Gene names: JW1296, b1303, pspF, ycjB
Sequence domains: Sigma-54 interaction domain
RNA polymerase sigma-54 factor Chain: M
Molecule details ›
Chain: M
Length: 581 amino acids
Theoretical weight: 62.84 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P06223 (Residues: 1-119, 120-305, 306-414, 415-477; Coverage: 100%)
Gene names: ntrA, rpoN
Sequence domains:
Non-template promoter DNA Chain: H
Molecule details ›
Chain: H
Length: 63 nucleotides
Theoretical weight: 19.4 KDa
Template promoter DNA Chain: I
Molecule details ›
Chain: I
Length: 63 nucleotides
Theoretical weight: 19.44 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 5.8Å
Relevant EMDB volumes: EMD-3696
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

6 review citations

AAA+ ATPases: structural insertions under the magnifying glass.
Jessop et al. (2021)
5 more

6 mentions without citation

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