› 6vvv

X-ray diffraction
3.2Å resolution

Crystal structure of a Mycobacterium smegmatis transcription initiation complex with Rifampicin-resistant RNA polymerase

Released:
DOI: 10.2210/pdb6vvv/pdb
PDB entry 6vvv coloured by chain, front view.
PDB entry 6vvv coloured by chain, side view.
PDB entry 6vvv coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Primary publication:
The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase.
Lilic M, Chen J, Boyaci H, Braffman N, Hubin EA, Herrmann J, Müller R, Mooney R, Landick R, Darst SA, Campbell EA
Proc Natl Acad Sci U S A 117 30423-30432 (2020)
PMID: 33199626

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)
PDBe Complex ID:
PDB-CPX-106295 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (8 distinct):
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 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: A0QZ11 (Residues: 1-114; Coverage: 100%)
Gene names: MSMEG_3858, MSMEI_3768, rbpA
Sequence domains: RNA polymerase-binding protein
DNA-directed RNA polymerase subunit alpha Chains: A, B, T
Molecule details ›
Chains: A, B, T
Length: 350 amino acids
Theoretical weight: 37.96 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
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: 128.71 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
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
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
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
UniProt:
  • Canonical: A0QW02 (Residues: 1-466; Coverage: 100%)
Gene names: MSMEG_2758, sigA
Sequence domains:
DNA (31-MER) Chain: O
Molecule details ›
Chain: O
Length: 31 nucleotides
Theoretical weight: 9.57 KDa
DNA (26-MER) Chain: P
Molecule details ›
Chain: P
Length: 26 nucleotides
Theoretical weight: 7.93 KDa

Ligands and Environments

2 bound ligands:
Ligand SO4 12 x SO4
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 129.748Å b: 162.344Å c: 137.155Å
α: 90° β: 111.27° γ: 90°
R-values:
R R work R free
0.235 0.234 0.262
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

2 review citations

M. tuberculosis Transcription Machinery: A Review on the Mycobacterial RNA Polymerase and Drug Discovery Efforts.
Stephanie et al. (2022)
1 more