Autophagy is a cellular process that degrades cytoplasmic components in lysosomes, helping cells survive nutrient deprivation. The mammalian target of rapamycin (mTOR) is a key regulator of autophagy, but its exact mechanism of action remains unclear. This study identifies a novel mammalian autophagy factor, Atg13, which forms a stable ~3-MDa complex with ULK1 and FIP200. Atg13 localizes to autophagosomal isolation membranes and is essential for autophagosome formation. Unlike yeast, the formation of the ULK1-Atg13-FIP200 complex is not affected by nutrient conditions. Importantly, mTORC1 is incorporated into this complex in a nutrient-dependent manner and phosphorylates ULK1 and Atg13. Rapamycin treatment or starvation leads to dephosphorylation of ULK1. These findings suggest that mTORC1 suppresses autophagy by directly regulating the ~3-MDa ULK1-Atg13-FIP200 complex. The study also shows that Atg13 is hyperphosphorylated under nutrient-rich conditions and partially dephosphorylated during starvation. Atg13 localizes to autophagosomal membranes and is required for autophagy. The ULK1-Atg13-FIP200 complex is a large protein complex that includes ULK1, Atg13, and FIP200. mTORC1 interacts with this complex under nutrient-rich conditions and is incorporated into it in a nutrient-dependent manner. mTOR phosphorylates ULK1 and Atg13, and ULK1 is dephosphorylated by rapamycin treatment or starvation. These results suggest that mTOR regulates autophagy through the ~3-MDa ULK1-Atg13-FIP200 complex. The study also shows that ULK1 phosphorylates Atg13, indicating that Atg13 can be phosphorylated by both mTOR and ULK1. The findings highlight the importance of the ULK1-Atg13-FIP200 complex in autophagy regulation and suggest that mTORC1 suppresses autophagy by directly interacting with this complex.Autophagy is a cellular process that degrades cytoplasmic components in lysosomes, helping cells survive nutrient deprivation. The mammalian target of rapamycin (mTOR) is a key regulator of autophagy, but its exact mechanism of action remains unclear. This study identifies a novel mammalian autophagy factor, Atg13, which forms a stable ~3-MDa complex with ULK1 and FIP200. Atg13 localizes to autophagosomal isolation membranes and is essential for autophagosome formation. Unlike yeast, the formation of the ULK1-Atg13-FIP200 complex is not affected by nutrient conditions. Importantly, mTORC1 is incorporated into this complex in a nutrient-dependent manner and phosphorylates ULK1 and Atg13. Rapamycin treatment or starvation leads to dephosphorylation of ULK1. These findings suggest that mTORC1 suppresses autophagy by directly regulating the ~3-MDa ULK1-Atg13-FIP200 complex. The study also shows that Atg13 is hyperphosphorylated under nutrient-rich conditions and partially dephosphorylated during starvation. Atg13 localizes to autophagosomal membranes and is required for autophagy. The ULK1-Atg13-FIP200 complex is a large protein complex that includes ULK1, Atg13, and FIP200. mTORC1 interacts with this complex under nutrient-rich conditions and is incorporated into it in a nutrient-dependent manner. mTOR phosphorylates ULK1 and Atg13, and ULK1 is dephosphorylated by rapamycin treatment or starvation. These results suggest that mTOR regulates autophagy through the ~3-MDa ULK1-Atg13-FIP200 complex. The study also shows that ULK1 phosphorylates Atg13, indicating that Atg13 can be phosphorylated by both mTOR and ULK1. The findings highlight the importance of the ULK1-Atg13-FIP200 complex in autophagy regulation and suggest that mTORC1 suppresses autophagy by directly interacting with this complex.