In yeast, the starvation-induced dephosphorylation of Atg13 enables it to form the Atg1 complex (comprising Atg1, Atg13, Atg17, Atg29 and Atg31); this complex is necessary to assemble the pre-autophagosomal structure (PAS) and thus to initiate autophagy. Fujioka et al. solved the structure of the Atg1 carboxy-terminal domain in complex with the minimum Atg1-binding region of Atg13, and of Atg17–Atg29–Atg31 in complex with the minimum Atg17-binding region of Atg13, using bacterial homologues of the yeast proteins. The analysis revealed that Atg1 harbours two tandem microtubule-interacting and transport domains that bind to Atg13. In Atg17 a hydrophobic pocket, and its surrounding acidic residues, comprise the Atg13-binding site. Importantly, dephosphorylation of Ser residues in Atg13 increased its interaction with Atg1 and Atg17, which explains how formation of the Atg1 complex, and thus of the PAS, is driven by starvation-induced dephosphorylation of Atg13.