› 6pmi

Electron Microscopy
3.86Å resolution

Sigm28-transcription initiation complex with specific promoter at the state 1

Released:
DOI: 10.2210/pdb6pmi/pdb
PDB entry 6pmi coloured by chain, front view.
PDB entry 6pmi coloured by chain, side view.
PDB entry 6pmi coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of bacterial σ28 -mediated transcription reveals roles of the RNA polymerase zinc-binding domain.
Shi W, Zhou W, Zhang B, Huang S, Jiang Y, Schammel A, Hu Y, Liu B
EMBO J 39 e104389 (2020)
PMID: 32484956
Related structures: EMD-20394

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)
Assembly name:
PDBe Complex ID:
PDB-CPX-199498 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
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 O157:H7
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 S88
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 O157:H7
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 S88
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 FliA Chain: F
Molecule details ›
Chain: F
Length: 247 amino acids
Theoretical weight: 28.63 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AEM6 (Residues: 1-239; Coverage: 100%)
Gene names: JW1907, b1922, flaD, fliA, rpoF
Sequence domains:
SYNTHETIC NONTEMPLATE STRAND DNA (54-MER) Chain: 1
Molecule details ›
Chain: 1
Length: 54 nucleotides
Theoretical weight: 16.56 KDa
SYNTHETIC TEMPLATE STRAND DNA (54-MER) Chain: 2
Molecule details ›
Chain: 2
Length: 54 nucleotides
Theoretical weight: 16.76 KDa
Nascent RNA Chain: 3
Molecule details ›
Chain: 3
Length: 3 nucleotides
Theoretical weight: 1.08 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.86Å
Relevant EMDB volumes: EMD-20394
Expression system: Escherichia coli

Quick links

Citations

2 review citations

M. tuberculosis Transcription Machinery: A Review on the Mycobacterial RNA Polymerase and Drug Discovery Efforts.
Stephanie et al. (2022)
1 more

5 mentions without citation

The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches.
Gerovac et al. (2021)
4 more