› 5uh5

X-ray diffraction
3.75Å resolution

Crystal structure of Mycobacterium tuberculosis transcription initiation complex containing 3 nt of RNA

Released:
DOI: 10.2210/pdb5uh5/pdb
PDB entry 5uh5 coloured by chain, front view.
PDB entry 5uh5 coloured by chain, side view.
PDB entry 5uh5 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition.
Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH
Mol Cell 66 169-179.e8 (2017)
PMID: 28392175

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-119210 (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: 347 amino acids
Theoretical weight: 37.75 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli
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
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
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
UniProt:
  • Canonical: P9WGY5 (Residues: 1-110; Coverage: 100%)
Gene names: MTCY21B4.07, Rv1390, rpoZ
Sequence domains: RNA polymerase Rpb6
RNA polymerase sigma factor SigA Chain: F
Molecule details ›
Chain: F
Length: 528 amino acids
Theoretical weight: 57.88 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli
UniProt:
  • Canonical: P9WGI1 (Residues: 1-528; Coverage: 100%)
Gene names: MTCY05A6.24, Rv2703, mysA, rpoD, rpoV, sigA
Sequence domains:
DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*G)-3') Chain: H
Molecule details ›
Chain: H
Length: 23 nucleotides
Theoretical weight: 7.16 KDa
DNA (5'-D(*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*G)-3') Chain: G
Molecule details ›
Chain: G
Length: 16 nucleotides
Theoretical weight: 4.9 KDa
RNA (5'-R(*GP*GP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 3 nucleotides
Theoretical weight: 975 Da

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
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 150.343Å b: 163.641Å c: 195.547Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.194 0.248
Expression system: Escherichia coli

Quick links

Citations

12 review citations

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

9 mentions without citation

Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition.
Lin et al. (2017)
8 more