› 8to8

Electron Microscopy
2.9Å resolution

Escherichia coli RNA polymerase unwinding intermediate (I1b) at the lambda PR promoter

Released:
DOI: 10.2210/pdb8to8/pdb
PDB entry 8to8 coloured by chain, front view.
PDB entry 8to8 coloured by chain, side view.
PDB entry 8to8 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.
Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA
Nat Struct Mol Biol (2024)
PMID: 38951624
Related structures: EMD-41439

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
PDBe Complex ID:
PDB-CPX-246555 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
DNA-directed RNA polymerase subunit alpha Chains: G, H, M
Molecule details ›
Chains: G, H, M
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: I
Molecule details ›
Chain: I
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: J
Molecule details ›
Chain: J
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: K
Molecule details ›
Chain: K
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 factor RpoD Chain: L
Molecule details ›
Chain: L
Length: 613 amino acids
Theoretical weight: 70.35 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Sequence domains:
Nontemplate strand of lamdba PR promoter DNA Chain: O
Molecule details ›
Chain: O
Length: 105 nucleotides
Theoretical weight: 32.6 KDa
Template strand of lamdba PR promoter DNA Chain: P
Molecule details ›
Chain: P
Length: 105 nucleotides
Theoretical weight: 32.18 KDa

Ligands and Environments

3 bound ligands:
Ligand 4QM 4 x 4QM
Ligand MG 1 x MG
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.9Å
Relevant EMDB volumes: EMD-41439
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

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