› 8reb

Electron Microscopy
3.4Å resolution

Cryo-EM structure of bacterial RNA polymerase-sigma54 initial transcribing complex - 6nt complex

Released:
DOI: 10.2210/pdb8reb/pdb
PDB entry 8reb coloured by chain, front view.
PDB entry 8reb coloured by chain, side view.
PDB entry 8reb coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of σ54 displacement and promoter escape in bacterial transcription.
Gao F, Ye F, Zhang B, Cronin N, Buck M, Zhang X
Proc Natl Acad Sci U S A 121 e2309670120 (2024)
PMID: 38170755
Related structures: EMD-19081

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
PDBe Complex ID:
PDB-CPX-242821 (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: 321 amino acids
Theoretical weight: 35.73 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A7Z4 (Residues: 4-324; Coverage: 98%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: C
Molecule details ›
Chain: C
Length: 1341 amino acids
Theoretical weight: 150.69 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A8V2 (Residues: 1-1341; 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: 1373 amino acids
Theoretical weight: 152.04 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A8T7 (Residues: 4-1376; Coverage: 98%)
Gene names: JW3951, b3988, rpoC, tabB
Sequence domains:
DNA-directed RNA polymerase subunit omega Chain: E
Molecule details ›
Chain: E
Length: 74 amino acids
Theoretical weight: 8.45 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P0A800 (Residues: 2-75; Coverage: 81%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma-54 factor Chain: M
Molecule details ›
Chain: M
Length: 350 amino acids
Theoretical weight: 39.37 KDa
Source organism: Klebsiella oxytoca
Expression system: Klebsiella oxytoca
UniProt:
  • Canonical: P06223 (Residues: 93-472; Coverage: 73%)
Gene names: ntrA, rpoN
Sequence domains:
DNA (43-MER) Chain: N
Molecule details ›
Chain: N
Length: 43 nucleotides
Theoretical weight: 13.17 KDa
DNA (52-MER) Chain: T
Molecule details ›
Chain: T
Length: 52 nucleotides
Theoretical weight: 16.09 KDa
RNA (5'-R(P*GP*CP*CP*GP*CP*G)-3') Chain: R
Molecule details ›
Chain: R
Length: 6 nucleotides
Theoretical weight: 1.91 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: 3.4Å
Relevant EMDB volumes: EMD-19081
Expression systems:
  • Escherichia coli K-12
  • Klebsiella oxytoca

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