› 8f1j

Electron Microscopy
2.6Å resolution

SigN RNA polymerase early-melted intermediate bound to mismatch DNA fragment dhsU36mm2 (-12A)

Released:
DOI: 10.2210/pdb8f1j/pdb
PDB entry 8f1j coloured by chain, front view.
PDB entry 8f1j coloured by chain, side view.
PDB entry 8f1j coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
A general mechanism for transcription bubble nucleation in bacteria.
Mueller AU, Chen J, Wu M, Chiu C, Nixon BT, Campbell EA, Darst SA
OpenAccess logo Proc Natl Acad Sci U S A 120 e2220874120 (2023)
PMID: 36972428
Related structures: EMD-28785

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 decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-199544 (preferred)
Entry contents:
5 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (7 distinct):
DNA-directed RNA polymerase subunit alpha Chains: G, H
Molecule details ›
Chains: G, H
Length: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli
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: I
Molecule details ›
Chain: I
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli
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: J
Molecule details ›
Chain: J
Length: 1430 amino acids
Theoretical weight: 158.11 KDa
Source organism: Escherichia coli
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: K
Molecule details ›
Chain: K
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Escherichia coli
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-54 factor Chain: M
Molecule details ›
Chain: M
Length: 480 amino acids
Theoretical weight: 54.41 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P24255 (Residues: 1-477; Coverage: 100%)
Gene names: JW3169, b3202, glnF, ntrA, rpoN
Sequence domains:
DNA (36-MER) Chains: A, C
Molecule details ›
Chains: A, C
Length: 36 nucleotides
Theoretical weight: 11.07 KDa
DNA (36-MER) Chains: B, D
Molecule details ›
Chains: B, D
Length: 36 nucleotides
Theoretical weight: 11.05 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: 2.6Å
Relevant EMDB volumes: EMD-28785
Expression system: Escherichia coli

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