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

X-ray diffraction
3.05Å resolution
PDB entry 6ccv coloured by chain, front view.
PDB entry 6ccv coloured by chain, side view.
PDB entry 6ccv coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Assembly composition:
hetero undecamer (preferred)
Entry contents: 7 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero undecamer
Accessible surface area: 147080.31 Å2
Buried surface area: 55977.13 Å2
Dissociation area: 454.77 Å2
Dissociation energy (ΔGdiss): -0.27 kcal/mol
Dissociation entropy (TΔSdiss): 10.44 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-106293

Macromolecules

DNA-directed RNA polymerase subunit alpha
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
Pfam:
InterPro:
CATH:
DNA-directed RNA polymerase subunit alpha in PDB entry 6ccv, assembly 1, front view.
DNA-directed RNA polymerase subunit alpha in PDB entry 6ccv, assembly 1, side view.
DNA-directed RNA polymerase subunit alpha in PDB entry 6ccv, assembly 1, top view.
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DNA-directed RNA polymerase subunit beta
Chain: C
Length: 1169 amino acids
Theoretical weight: 128.68 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: P60281 (Residues: 1-1169; Coverage: 100%)
Gene names: MSMEG_1367, MSMEI_1328, rpoB
Pfam:
InterPro:
DNA-directed RNA polymerase subunit beta in PDB entry 6ccv, assembly 1, front view.
DNA-directed RNA polymerase subunit beta in PDB entry 6ccv, assembly 1, side view.
DNA-directed RNA polymerase subunit beta in PDB entry 6ccv, assembly 1, top view.
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DNA-directed RNA polymerase subunit beta'
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
Pfam:
InterPro:
DNA-directed RNA polymerase subunit beta' in PDB entry 6ccv, assembly 1, front view.
DNA-directed RNA polymerase subunit beta' in PDB entry 6ccv, assembly 1, side view.
DNA-directed RNA polymerase subunit beta' in PDB entry 6ccv, assembly 1, top view.
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DNA-directed RNA polymerase subunit omega
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
Pfam: RNA polymerase Rpb6
InterPro:
DNA-directed RNA polymerase subunit omega in PDB entry 6ccv, assembly 1, front view.
DNA-directed RNA polymerase subunit omega in PDB entry 6ccv, assembly 1, side view.
DNA-directed RNA polymerase subunit omega in PDB entry 6ccv, assembly 1, top view.
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RNA polymerase sigma factor SigA
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
Pfam:
InterPro:
RNA polymerase sigma factor SigA in PDB entry 6ccv, assembly 1, front view.
RNA polymerase sigma factor SigA in PDB entry 6ccv, assembly 1, side view.
RNA polymerase sigma factor SigA in PDB entry 6ccv, assembly 1, top view.
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Unknown Peptide
Chain: G
Length: 17 amino acids
Theoretical weight: 1.46 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
Expression system: Escherichia coli
Unknown Peptide in PDB entry 6ccv, assembly 1, front view.
Unknown Peptide in PDB entry 6ccv, assembly 1, side view.
Unknown Peptide in PDB entry 6ccv, assembly 1, top view.
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RNA polymerase-binding protein RbpA
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
Pfam: RNA polymerase-binding protein
InterPro:
RNA polymerase-binding protein RbpA in PDB entry 6ccv, assembly 1, front view.
RNA polymerase-binding protein RbpA in PDB entry 6ccv, assembly 1, side view.
RNA polymerase-binding protein RbpA in PDB entry 6ccv, assembly 1, top view.
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DNA chain O
Name: DNA (31-MER)
Representative chains: O
Length: 31 nucleotides
Theoretical weight: 9.57 KDa
DNA (31-MER) in PDB entry 6ccv, assembly 1, front view.
DNA (31-MER) in PDB entry 6ccv, assembly 1, side view.
DNA (31-MER) in PDB entry 6ccv, assembly 1, top view.
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DNA chain P
Name: DNA (26-MER)
Representative chains: P
Length: 26 nucleotides
Theoretical weight: 7.93 KDa
DNA (26-MER) in PDB entry 6ccv, assembly 1, front view.
DNA (26-MER) in PDB entry 6ccv, assembly 1, side view.
DNA (26-MER) in PDB entry 6ccv, assembly 1, top view.
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