› 5i4q

X-ray diffraction
2.35Å resolution

Contact-dependent inhibition system from Escherichia coli NC101 - ternary CdiA/CdiI/EF-Tu complex (domains 2 and 3)

Released:
DOI: 10.2210/pdb5i4q/pdb
PDB entry 5i4q coloured by chain, front view.
PDB entry 5i4q coloured by chain, side view.
PDB entry 5i4q coloured by chain, top view.
Source organisms:
Primary publication:
Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs.
Michalska K, Gucinski GC, Garza-Sánchez F, Johnson PM, Stols LM, Eschenfeldt WH, Babnigg G, Low DA, Goulding CW, Joachimiak A, Hayes CS
Nucleic Acids Res 45 10306-10320 (2017)
PMID: 28973472

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-143215 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
tRNA nuclease CdiA Chain: A
Molecule details ›
Chain: A
Length: 92 amino acids
Theoretical weight: 10.48 KDa
Source organism: Escherichia coli NC101
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DSI1 (Residues: 3198-3289; Coverage: 3%)
Gene names: ECNC101_09164, cdiA
Immunity protein CdiI Chain: B
Molecule details ›
Chain: B
Length: 114 amino acids
Theoretical weight: 14.23 KDa
Source organism: Escherichia coli NC101
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0DSM8 (Residues: 1-106; Coverage: 100%)
Gene names: ECNC101_09169, cdiI
Elongation factor Tu 1 Chain: C
Molecule details ›
Chain: C
Length: 217 amino acids
Theoretical weight: 23.92 KDa
Source organism: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0CE47 (Residues: 178-394; Coverage: 55%)
Gene names: JW3301, b3339, tufA
Sequence domains:
Structure domains: Translation factors

Ligands and Environments

2 bound ligands:
Ligand CL 1 x CL
Ligand SO4 1 x SO4
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P4212
Unit cell:
a: 131.155Å b: 131.155Å c: 63.327Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.181 0.218
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Polymorphic Toxins and Their Immunity Proteins: Diversity, Evolution, and Mechanisms of Delivery.
Ruhe et al. (2020)
3 more

5 mentions without citation

Functional and Structural Diversity of Bacterial Contact-Dependent Growth Inhibition Effectors.
Cuthbert et al. (2022)
4 more