› 6dv9

X-ray diffraction
3.8Å resolution

Crystal structure of Mycobacterium tuberculosis transcription initiation complex(ECF sigma factor L) containing 5nt RNA with 4nt spacer

Released:
DOI: 10.2210/pdb6dv9/pdb
PDB entry 6dv9 coloured by chain, front view.
PDB entry 6dv9 coloured by chain, side view.
PDB entry 6dv9 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Structural basis of ECF-σ-factor-dependent transcription initiation.
Lin W, Mandal S, Degen D, Cho MS, Feng Y, Das K, Ebright RH
Nat Commun 10 710 (2019)
PMID: 30755604

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)
PDBe Complex ID:
PDB-CPX-119811 (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: 359 amino acids
Theoretical weight: 39.32 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P9WGZ1 (Residues: 1-347; Coverage: 100%)
Gene names: MTCY13E12.10c, Rv3457c, rpoA
Sequence domains:
Structure domains:
DNA-directed RNA polymerase subunit beta Chain: C
Molecule details ›
Chain: C
Length: 1178 amino acids
Theoretical weight: 130.02 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P9WGY9 (Residues: 1-1178; Coverage: 100%)
Gene names: MTCI376.08c, Rv0667, rpoB
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chain: D
Molecule details ›
Chain: D
Length: 1316 amino acids
Theoretical weight: 146.97 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P9WGY7 (Residues: 1-1316; Coverage: 100%)
Gene names: MTCI376.07c, Rv0668, rpoC
Sequence domains:
DNA-directed RNA polymerase subunit omega Chain: E
Molecule details ›
Chain: E
Length: 110 amino acids
Theoretical weight: 11.85 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P9WGY5 (Residues: 1-110; Coverage: 100%)
Gene names: MTCY21B4.07, Rv1390, rpoZ
Sequence domains: RNA polymerase Rpb6
ECF RNA polymerase sigma factor SigL Chain: F
Molecule details ›
Chain: F
Length: 177 amino acids
Theoretical weight: 19.56 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P9WGH5 (Residues: 1-177; Coverage: 100%)
Gene names: Rv0735, sigL
Sequence domains:
DNA (5'-D(*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*G)-3') Chain: G
Molecule details ›
Chain: G
Length: 17 nucleotides
Theoretical weight: 5.27 KDa
DNA (5'-D(P*CP*GP*TP*GP*TP*CP*AP*GP*AP*GP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*C)-3') Chain: H
Molecule details ›
Chain: H
Length: 22 nucleotides
Theoretical weight: 6.81 KDa
RNA (5'-R(*CP*UP*CP*GP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 5 nucleotides
Theoretical weight: 1.55 KDa

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 143.27Å b: 161.44Å c: 237.69Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.184 0.232
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'

Quick links

Citations

5 review citations

Diverse and unified mechanisms of transcription initiation in bacteria.
Chen et al. (2021)
4 more

3 mentions without citation

Structural basis of ECF-σ-factor-dependent transcription initiation.
Lin et al. (2019)
2 more