› 6l8e

X-ray diffraction
2.35Å resolution

Crystal structure of heterohexameric YoeB-YefM complex bound to 26bp-DNA

Released:
DOI: 10.2210/pdb6l8e/pdb
PDB entry 6l8e coloured by chain, front view.
PDB entry 6l8e coloured by chain, side view.
PDB entry 6l8e coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
Primary publication:
Distinct oligomeric structures of the YoeB-YefM complex provide insights into the conditional cooperativity of type II toxin-antitoxin system.
Xue L, Yue J, Ke J, Khan MH, Wen W, Sun B, Zhu Z, Niu L
Nucleic Acids Res 48 10527-10541 (2020)
PMID: 32845304

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120195 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
Antitoxin Chains: A, B, C, D, I, J, K, L
Molecule details ›
Chains: A, B, C, D, I, J, K, L
Length: 83 amino acids
Theoretical weight: 9.44 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q2G285 (Residues: 1-83; Coverage: 100%)
Gene name: SAOUHSC_02692
Sequence domains: Antitoxin Phd_YefM, type II toxin-antitoxin system
Putative mRNA interferase YoeB Chains: E, F, M, N
Molecule details ›
Chains: E, F, M, N
Length: 88 amino acids
Theoretical weight: 10.46 KDa
Source organism: Staphylococcus aureus subsp. aureus NCTC 8325
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q2G286 (Residues: 1-88; Coverage: 100%)
Gene name: SAOUHSC_02691
Sequence domains: YoeB-like toxin of bacterial type II toxin-antitoxin system
DNA (26-mer) Chains: G, O
Molecule details ›
Chains: G, O
Length: 26 nucleotides
Theoretical weight: 8.01 KDa
DNA (26-mer) Chains: H, P
Molecule details ›
Chains: H, P
Length: 26 nucleotides
Theoretical weight: 7.96 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P43212
Unit cell:
a: 151.352Å b: 151.352Å c: 183.778Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.197 0.222
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Prokaryote toxin-antitoxin modules: Complex regulation of an unclear function.
De Bruyn et al. (2021)
9 other articles

1 mention without citation

Distinct oligomeric structures of the YoeB-YefM complex provide insights into the conditional cooperativity of type II toxin-antitoxin system.
Xue et al. (2020)