The ULK-Atg13-FIP200 complex mediates mTOR signaling to the autophagy machinery. This study identifies that mTOR phosphorylates a mammalian homologue of Atg13 and the mammalian Atg1 homologues ULK1 and ULK2. The mammalian Atg13 binds both ULK1 and ULK2 and mediates the interaction of the ULK proteins with FIP200. The binding of Atg13 stabilizes and activates ULK and facilitates the phosphorylation of FIP200 by ULK, whereas knockdown of Atg13 inhibits autophagosome formation. Inhibition of mTOR by rapamycin or leucine deprivation leads to dephosphorylation of ULK1, ULK2, and Atg13 and activates ULK to phosphorylate FIP200. These findings demonstrate that the ULK-Atg13-FIP200 complexes are direct targets of mTOR and important regulators of autophagy in response to mTOR signaling. The study also shows that Atg13 is important for the ULK1 kinase activity and FIP200 phosphorylation by ULKs. The results suggest that Atg13 plays a positive role in mTOR-regulated autophagy processes by enhancing the catalytic activity of ULK and allowing ULK to phosphorylate FIP200, the protein crucial for autophagosome formation. The study provides important findings regarding the function of Atg13, including its role in mediating the interaction between ULK and FIP200, thereby forming two protein complexes: ULK1-Atg13-FIP200 and ULK2-Atg13-FIP200. The study also shows that ULK1 and ULK2 have different binding affinities toward Atg13 and FIP200, and that the interaction between ULK2 and Atg13 is only detected in the presence of FIP200. These findings suggest that the ULK-Atg13-FIP200 complexes are important for autophagy regulation and that Atg13 plays a key role in this process.The ULK-Atg13-FIP200 complex mediates mTOR signaling to the autophagy machinery. This study identifies that mTOR phosphorylates a mammalian homologue of Atg13 and the mammalian Atg1 homologues ULK1 and ULK2. The mammalian Atg13 binds both ULK1 and ULK2 and mediates the interaction of the ULK proteins with FIP200. The binding of Atg13 stabilizes and activates ULK and facilitates the phosphorylation of FIP200 by ULK, whereas knockdown of Atg13 inhibits autophagosome formation. Inhibition of mTOR by rapamycin or leucine deprivation leads to dephosphorylation of ULK1, ULK2, and Atg13 and activates ULK to phosphorylate FIP200. These findings demonstrate that the ULK-Atg13-FIP200 complexes are direct targets of mTOR and important regulators of autophagy in response to mTOR signaling. The study also shows that Atg13 is important for the ULK1 kinase activity and FIP200 phosphorylation by ULKs. The results suggest that Atg13 plays a positive role in mTOR-regulated autophagy processes by enhancing the catalytic activity of ULK and allowing ULK to phosphorylate FIP200, the protein crucial for autophagosome formation. The study provides important findings regarding the function of Atg13, including its role in mediating the interaction between ULK and FIP200, thereby forming two protein complexes: ULK1-Atg13-FIP200 and ULK2-Atg13-FIP200. The study also shows that ULK1 and ULK2 have different binding affinities toward Atg13 and FIP200, and that the interaction between ULK2 and Atg13 is only detected in the presence of FIP200. These findings suggest that the ULK-Atg13-FIP200 complexes are important for autophagy regulation and that Atg13 plays a key role in this process.