The molecular mechanism of switching between phosphotransferase- and phosphatase-competent states in histidine-kinases was uncovered, through direct crystallographic observation of a bona fide complex between a histidine-kinase (HK) and its response regulator (RR) from Bacillus subtilis. This HK:RR binary complex was crystallised in two different signalling states by using state-stabilising point-mutants of the kinase. To the best of our knowledge these are the first near-atomic resolution structures of such complexes from a mesophilic bacterial species.