› 6kop

X-ray diffraction
3.3Å resolution

Mycobacterium tuberculosis initial transcription complex comprising sigma H and 5'-OH RNA of 9 nt

Released:
DOI: 10.2210/pdb6kop/pdb
PDB entry 6kop coloured by chain, front view.
PDB entry 6kop coloured by chain, side view.
PDB entry 6kop coloured by chain, top view.
Source organism: Mycobacterium tuberculosis H37Rv
Primary publication:
RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Li L, Molodtsov V, Lin W, Ebright RH, Zhang Y
Proc Natl Acad Sci U S A 117 5801-5809 (2020)
PMID: 32127479

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-120165 (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:
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 (5'-D(*TP*TP*GP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*A)-3') Chain: G
Molecule details ›
Chain: G
Length: 23 nucleotides
Theoretical weight: 7.15 KDa
DNA (5'-D(*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*GP*TP*G)-3') Chain: H
Molecule details ›
Chain: H
Length: 21 nucleotides
Theoretical weight: 6.54 KDa
RNA (5'-R(*CP*AP*CP*CP*CP*UP*CP*GP*A)-3') Chain: I
Molecule details ›
Chain: I
Length: 9 nucleotides
Theoretical weight: 2.79 KDa

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: SSRF BEAMLINE BL17U1
Spacegroup: P21
Unit cell:
a: 127.371Å b: 162.637Å c: 133.421Å
α: 90° β: 117.95° γ: 90°
R-values:
R R work R free
0.218 0.217 0.255
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

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

2 mentions without citation

RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
Li et al. (2020)
1 more