› 6n58

Electron Microscopy
3.78Å resolution

Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation II

Released:
DOI: 10.2210/pdb6n58/pdb
PDB entry 6n58 coloured by chain, front view.
PDB entry 6n58 coloured by chain, side view.
PDB entry 6n58 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
E. coli TraR allosterically regulates transcription initiation by altering RNA polymerase conformation.
Chen J, Gopalkrishnan S, Chiu C, Chen AY, Campbell EA, Gourse RL, Ross W, Darst SA
OpenAccess logo Elife 8 (2019)
PMID: 31841111
Related structures: EMD-0349

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 heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132732 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 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 BL21(DE3)
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 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: 1430 amino acids
Theoretical weight: 158.07 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
RNA polymerase sigma factor RpoD Chain: L
Molecule details ›
Chain: L
Length: 616 amino acids
Theoretical weight: 70.72 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Sequence domains:
Protein TraR Chain: M
Molecule details ›
Chain: M
Length: 72 amino acids
Theoretical weight: 8.19 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P41065 (Residues: 2-73; Coverage: 99%)
Gene names: ECOK12F083, traR
Sequence domains: Prokaryotic dksA/traR C4-type zinc finger

Ligands and Environments

3 bound ligands:
Ligand 1N7 4 x 1N7
Ligand MG 1 x MG
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.78Å
Relevant EMDB volumes: EMD-0349
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 review citations

Causes and consequences of RNA polymerase II stalling during transcript elongation.
Noe Gonzalez et al. (2021)
9 more

4 mentions without citation

Using cryo-EM to uncover mechanisms of bacterial transcriptional regulation.
Wood et al. (2021)
3 more