› 8pil

Electron Microscopy
3.2Å resolution

E. coli transcription complex paused at ops site and bound to RfaH and NusA

Released:
DOI: 10.2210/pdb8pil/pdb
PDB entry 8pil coloured by chain, front view.
PDB entry 8pil coloured by chain, side view.
PDB entry 8pil coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
Concerted transformation of a hyper-paused transcription complex and its reinforcing protein.
Zuber PK, Said N, Hilal T, Wang B, Loll B, González-Higueras J, Ramírez-Sarmiento CA, Belogurov GA, Artsimovitch I, Wahl MC, Knauer SH
OpenAccess logo Nat Commun 15 3040 (2024)
PMID: 38589445
Related structures: EMD-17685

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 decamer (preferred)
PDBe Complex ID:
PDB-CPX-243367 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (9 distinct):
Transcription antitermination protein RfaH Chain: P
Molecule details ›
Chain: P
Length: 164 amino acids
Theoretical weight: 18.56 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AFW0 (Residues: 1-162; Coverage: 100%)
Gene names: JW3818, b3842, hlyT, rfaH, sfrB
Sequence domains: Transcription termination factor nusG
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 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: J
Molecule details ›
Chain: J
Length: 1416 amino acids
Theoretical weight: 156.5 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A8T7 (Residues: 2-1407; 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 BL21(DE3)
UniProt:
  • Canonical: P0A800 (Residues: 1-91; Coverage: 100%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
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 BL21(DE3)
UniProt:
  • Canonical: P0A7Z4 (Residues: 1-329; Coverage: 100%)
Gene names: JW3257, b3295, pez, phs, rpoA, sez
Sequence domains:
Transcription termination/antitermination protein NusA Chain: F
Molecule details ›
Chain: F
Length: 497 amino acids
Theoretical weight: 55.09 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AFF6 (Residues: 1-495; Coverage: 100%)
Gene names: JW3138, b3169, nusA
Sequence domains:
non-template DNA Chain: A
Molecule details ›
Chain: A
Length: 40 nucleotides
Theoretical weight: 12.21 KDa
template DNA Chain: B
Molecule details ›
Chain: B
Length: 40 nucleotides
Theoretical weight: 12.42 KDa
RNA Chain: R
Molecule details ›
Chain: R
Length: 17 nucleotides
Theoretical weight: 5.41 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: 3.2Å
Relevant EMDB volumes: EMD-17685
Expression system: Escherichia coli BL21(DE3)

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