The mechanistic target of rapamycin complex 1 (mTORC1) couples cell growth to nutrient, energy and growth factor availability (1–3). mTORC1 is activated at the lysosomal membrane when amino acids are replete via the Rag guanosine triphosphatases (GTPases) (4–6). Rags exist in two stable states, an inactive (RagA/B GDP :RagC/D GTP ) and active (RagA/B GTP :RagC/D GDP ) state, during low and high cellular amino acid levels (4, 5). The lysosomal folliculin (FLCN) complex (LFC) consists of the inactive Rag dimer, the pentameric scaffold Ragulator (7, 8), and the FLCN:FNIP (FLCN-interacting protein) GTPase activating protein (GAP) complex (9), and prevents activation of the Rag dimer during amino acid starvation (10, 11). How the LFC is released upon amino acid refeeding is a major outstanding question in amino-acid dependent Rag activation. Here we show that the cytoplasmic tail of the lysosomal solute carrier family 38 member 9 (SLC38A9), a known Rag activator (12–14), destabilizes the LFC. By breaking up the LFC, SLC38A9 triggers the GAP activity of FLCN:FNIP toward RagC. We present the cryo electron microscopy (cryo-EM) structures of Rags in complex with their lysosomal anchor complex Ragulator and the cytoplasmic tail of SLC38A9 in the pre and post GTP hydrolysis state of RagC, which explain how SLC38A9 destabilizes the LFC and so promotes Rag dimer activation.

Structural mechanism for amino acid-dependent Rag GTPase switching by SLC38A9