The toxin-antitoxin system is ubiquitously existed in bacteria and archaea, performing a wide variety of functions modulating cell fitness in response to environmental cues. In this report, we solved the crystal structure of the toxin-antitoxin HigBA complex from E. coli K-12 to 2.7 angstrom resolution. The crystal structure of the HigBA complex displays a hetero-tetramer (HigBA)(2) form comprised by two HigB and two HigA subunits. Each toxin HigB resumes a microbial RNase T1 fold, characteristic of a three antiparallel beta-sheet core shielded by a few alpha-helices at either side. Each antitoxin HigA composed of all alpha-helices resembles a "C"-shaped clamp nicely encompassing a HigB in the (HigBA)(2) complex. Two HigA monomers dimerize at their N-terminal domain. We showed that HigA helix alpha 1 was essential for HigA dimerization and the hetero-tetramer (HigBA)(2) formation, but not for a hetero-dimeric HigBA formation. HigA dimerization mediated by helix alpha 1 was dispensable for DNA-binding, as a heterodimeric HigBA complex still bound to the higBA operator in vitro. The HigA C-terminal domain with a helix-turn-helix fold was essential for DNA binding. We also defined two palindromes in higBA operator specifically recognized by HigA and HigBA in vitro. (C) 2016 Elsevier Inc. All rights reserved.