› 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 5i4q coloured by chain and viewed from the front.
PDB 5i4q coloured by chain and viewed from the side.
PDB 5i4q coloured by chain and viewed from the top.
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-S��nchez 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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (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

3 review citations

Contact-Dependent Growth Inhibition in Bacteria: Do Not Get Too Close!
Ikryannikova et al. (2020)
2 more

4 mentions without citation

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