› 8r3m

Electron Microscopy
3.49Å resolution

Mycobacterium smegnatis RNA polymerase transcription initiation complex with SigmaA, RbpA, HelD N-terminal, CO and PCh loop domain, and an upstream-fork promoter fragment; State III conformation

Released:
DOI: 10.2210/pdb8r3m/pdb
PDB entry 8r3m coloured by chain, front view.
PDB entry 8r3m coloured by chain, side view.
PDB entry 8r3m coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Entry authors: Koval T, Krasny L, Dohnalek J, Kouba T
Related structures: EMD-18873

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-269772 (preferred)
Entry contents:
7 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (9 distinct):
DNA-directed RNA polymerase subunit alpha Chains: A, B
Molecule details ›
Chains: A, B
Length: 350 amino acids
Theoretical weight: 37.96 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli
UniProt:
  • Canonical: A0QSL8 (Residues: 1-350; Coverage: 100%)
Gene names: MSMEG_1524, MSMEI_1488, rpoA
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: C
Molecule details ›
Chain: C
Length: 1169 amino acids
Theoretical weight: 128.68 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli
UniProt:
  • Canonical: P60281 (Residues: 1-1169; Coverage: 100%)
Gene names: MSMEG_1367, MSMEI_1328, rpoB
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chain: D
Molecule details ›
Chain: D
Length: 1317 amino acids
Theoretical weight: 146.71 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli
UniProt:
  • Canonical: A0QS66 (Residues: 1-1317; Coverage: 100%)
Gene names: MSMEG_1368, MSMEI_1329, rpoC
Sequence domains:
DNA-directed RNA polymerase subunit omega Chain: E
Molecule details ›
Chain: E
Length: 107 amino acids
Theoretical weight: 11.54 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli
UniProt:
  • Canonical: A0QWT1 (Residues: 1-107; Coverage: 100%)
Gene names: MSMEG_3053, MSMEI_2977, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor SigA Chain: F
Molecule details ›
Chain: F
Length: 466 amino acids
Theoretical weight: 51.57 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli
UniProt:
  • Canonical: A0QW02 (Residues: 1-466; Coverage: 100%)
Gene names: MSMEG_2758, sigA
Sequence domains:
RNA polymerase-binding protein RbpA Chain: J
Molecule details ›
Chain: J
Length: 114 amino acids
Theoretical weight: 13.08 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli
UniProt:
  • Canonical: A0QZ11 (Residues: 1-114; Coverage: 100%)
Gene names: MSMEG_3858, MSMEI_3768, rbpA
Sequence domains: RNA polymerase-binding protein
UvrD-like helicase ATP-binding domain-containing protein Chain: H
Molecule details ›
Chain: H
Length: 736 amino acids
Theoretical weight: 81.3 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli
UniProt:
  • Canonical: I7G5V9 (Residues: 1-736; Coverage: 100%)
Gene name: MSMEI_2121
Sequence domains: UvrD/REP helicase N-terminal domain
DNA 31-MER Chain: O
Molecule details ›
Chain: O
Length: 31 nucleotides
Theoretical weight: 9.57 KDa
DNA 22-MER Chain: P
Molecule details ›
Chain: P
Length: 22 nucleotides
Theoretical weight: 6.69 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: 3.49Å
Relevant EMDB volumes: EMD-18873
Expression system: Escherichia coli

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