› 5zx2

X-ray diffraction
2.8Å resolution

Mycobacterium tuberculosis RNA polymerase transcription initiation complex with ECF sigma factor sigma H and 7nt RNA

Released:
DOI: 10.2210/pdb5zx2/pdb
PDB entry 5zx2 coloured by chain, front view.
PDB entry 5zx2 coloured by chain, side view.
PDB entry 5zx2 coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
Structural basis for transcription initiation by bacterial ECF σ factors.
Li L, Fang C, Zhuang N, Wang T, Zhang Y
Nat Commun 10 1153 (2019)
PMID: 30858373

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-119536 (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: 368 amino acids
Theoretical weight: 40.28 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
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: 1174 amino acids
Theoretical weight: 129.6 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WGY9 (Residues: 7-1178; Coverage: 100%)
Gene names: MTCI376.08c, Rv0667, rpoB
Sequence domains:
DNA-directed RNA polymerase subunit beta' Chain: D
Molecule details ›
Chain: D
Length: 1317 amino acids
Theoretical weight: 147.07 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WGY7 (Residues: 2-1316; 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(DE3)
UniProt:
  • Canonical: P9WGY5 (Residues: 1-110; Coverage: 100%)
Gene names: MTCY21B4.07, Rv1390, rpoZ
Sequence domains: RNA polymerase Rpb6
ECF RNA polymerase sigma factor SigH Chain: F
Molecule details ›
Chain: F
Length: 218 amino acids
Theoretical weight: 24.38 KDa
Source organism: Mycobacterium tuberculosis H37Rv
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P9WGH9 (Residues: 1-216; Coverage: 100%)
Gene names: MTCY07D11.03, Rv3223c, rpoE, sigH
Sequence domains:
DNA (48-MER) Chain: G
Molecule details ›
Chain: G
Length: 48 nucleotides
Theoretical weight: 14.85 KDa
DNA (47-MER) Chain: H
Molecule details ›
Chain: H
Length: 47 nucleotides
Theoretical weight: 14.58 KDa
RNA (5'-R(*CP*CP*CP*UP*CP*GP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 7 nucleotides
Theoretical weight: 2.16 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P212121
Unit cell:
a: 129.824Å b: 164.027Å c: 214.792Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.22 0.255
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

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

7 mentions without citation

Structures and mechanism of transcription initiation by bacterial ECF factors.
Fang et al. (2019)
6 more