› 6xll

Electron Microscopy
2.7Å resolution

Cryo-EM structure of E. coli RNAP-promoter initial transcribing complex with 5-nt RNA transcript (RPitc-5nt)

Released:
DOI: 10.2210/pdb6xll/pdb
PDB entry 6xll coloured by chain, front view.
PDB entry 6xll coloured by chain, side view.
PDB entry 6xll coloured by chain, top view.
Source organism: Escherichia coli O157:H7
Primary publication:
Structural visualization of transcription activated by a multidrug-sensing MerR family regulator.
Yang Y, Liu C, Zhou W, Shi W, Chen M, Zhang B, Schatz DG, Hu Y, Liu B
Nat Commun 12 2702 (2021)
PMID: 33976201
Related structures: EMD-22247

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 nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120966 (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: 329 amino acids
Theoretical weight: 36.56 KDa
Source organism: Escherichia coli O157:H7
Expression system: Escherichia coli O157:H7
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: C
Molecule details ›
Chain: C
Length: 1342 amino acids
Theoretical weight: 150.82 KDa
Source organism: Escherichia coli O157:H7
Expression system: Escherichia coli O157:H7
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: D
Molecule details ›
Chain: D
Length: 1407 amino acids
Theoretical weight: 155.37 KDa
Source organism: Escherichia coli O157:H7
Expression system: Escherichia coli O157:H7
UniProt:
  • Canonical: P0A8T7 (Residues: 1-1407; Coverage: 100%)
Gene names: JW3951, b3988, rpoC, tabB
Sequence domains:
DNA-directed RNA polymerase subunit omega Chain: E
Molecule details ›
Chain: E
Length: 91 amino acids
Theoretical weight: 10.25 KDa
Source organism: Escherichia coli O157:H7
Expression system: Escherichia coli O157:H7
UniProt:
  • Canonical: P0A800 (Residues: 1-91; Coverage: 100%)
Gene names: JW3624, b3649, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor RpoD Chain: F
Molecule details ›
Chain: F
Length: 613 amino acids
Theoretical weight: 70.35 KDa
Source organism: Escherichia coli O157:H7
Expression system: Escherichia coli O157:H7
UniProt:
  • Canonical: P00579 (Residues: 1-613; Coverage: 100%)
Gene names: JW3039, alt, b3067, rpoD
Sequence domains:
synthetic non-template strand DNA (54-MER) Chain: N
Molecule details ›
Chain: N
Length: 54 nucleotides
Theoretical weight: 16.72 KDa
synthetic template strand DNA (54-MER) Chain: T
Molecule details ›
Chain: T
Length: 54 nucleotides
Theoretical weight: 16.56 KDa
RNA transcript (5-MER) Chain: R
Molecule details ›
Chain: R
Length: 5 nucleotides
Theoretical weight: 1.75 KDa

Ligands and Environments

3 bound ligands:
Ligand 1N7 2 x 1N7
Ligand MG 1 x MG
Ligand ZN 2 x ZN
1 modified residue:
Ligand GTP 1 x GTP

Experiments and Validation Details

Entry percentile scores
Resolution: 2.7Å
Relevant EMDB volumes: EMD-22247
Expression system: Escherichia coli O157:H7

Quick links

Citations

2 review citations

Bacterial MerR family transcription regulators: activationby distortion.
Fang et al. (2022)
1 more

2 mentions without citation

Structural visualization of transcription activated by a multidrug-sensing MerR family regulator.
Yang et al. (2021)
1 more