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During autophagy, a double membrane-bound structure called an autophagosome is generated,which sequesters degradation targets and delivers them to lysosomes/vacuole for degradation.Starvation strongly induces autophagy, and 18 Atg proteins have been shown to mediate autophagosome formation upon starvation in yeast.Most of them are localized to the pre-autophagosomal structure (PAS), from which autophagosomes are believed to be generated.PAS assembly requires the formation of the Atg1-Atg13-Atg17-Atg29-Atg31 complex (Atg1 complex), for which starvation-induced dephosphorylation of Atg13 is required.However, the molecular details underlying these events have not been established.Here we studied the Atg13-mediated interactions constructing the Atg1 complex by X-ray crystallography.Atg13 binds to two tandem microtubule interacting and transport (MIT) domains in Atg1 using an elongated helix-loop-helix region.Atg13 also binds to the N-terminal acidic pocket in Atg17 using a short basic region.Since Atg29 and Atg31 constitutively bind to Atg17, these Atg13-mediated interactions lead to the construction of the pentameric Atg1 complex.Biochemical and cell biological studies revealed that these interactions are accomplished only when specific serine residues of Atg13 are dephosphorylated, which explains why starvation initiates the PAS assembly and thus autophagy.