› 3tnd

X-ray diffraction
2.7Å resolution

Crystal structure of Shigella flexneri VapBC toxin-antitoxin complex

Released:
DOI: 10.2210/pdb3tnd/pdb
PDB entry 3tnd coloured by chain, front view.
PDB entry 3tnd coloured by chain, side view.
PDB entry 3tnd coloured by chain, top view.
Source organism: Shigella flexneri
Primary publication:
Crystal structure of the VapBC toxin-antitoxin complex from Shigella flexneri reveals a hetero-octameric DNA-binding assembly.
Dienemann C, Bøggild A, Winther KS, Gerdes K, Brodersen DE
J Mol Biol 414 713-22 (2011)
PMID: 22037005

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126529 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
tRNA(fMet)-specific endonuclease VapC Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 132 amino acids
Theoretical weight: 14.84 KDa
Source organism: Shigella flexneri
Expression system: Escherichia coli
UniProt:
  • Canonical: O06662 (Residues: 1-132; Coverage: 100%)
Gene names: CP0245, mvpA, stborf2, vapC
Sequence domains: PIN domain
Structure domains: 5'-nuclease
Antitoxin VapB Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 81 amino acids
Theoretical weight: 9.4 KDa
Source organism: Shigella flexneri
Expression system: Escherichia coli
UniProt:
  • Canonical: O06663 (Residues: 2-75; Coverage: 99%)
Gene names: CP0246, vapB
Structure domains: Pemi-like Protein 1; Chain: D

Ligands and Environments

2 bound ligands:
Ligand SO4 11 x SO4
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1, MAX II BEAMLINE I911-2
Spacegroup: P6122
Unit cell:
a: 91.403Å b: 91.403Å c: 549.09Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.185 0.182 0.238
Expression system: Escherichia coli

Quick links

Citations

16 review citations

Toxin-antitoxin systems in bacterial growth arrest and persistence.
Page et al. (2016)
15 more

12 mentions without citation

Structure, Biology, and Therapeutic Application of Toxin-Antitoxin Systems in Pathogenic Bacteria.
Lee et al. (2016)
11 more