The Rag GTPases (Rags) recruit mTORC1 to the lysosomal membrane in response to nutrients, where it is then activated in response to energy and growth factor availability. The lysosomal folliculin (FLCN) complex (LFC) consists of the inactive Rag dimer, the pentameric scaffold Ragulator, and the FLCN:FNIP2 (FLCN-interacting protein 2) GTPase activating protein (GAP) complex, and prevents Rag dimer activation during amino acid starvation. How the LFC is disassembled upon amino acid refeeding is an outstanding question. Here we show that the cytoplasmic tail of the human lysosomal solute carrier family 38 member 9 (SLC38A9) destabilizes the LFC and thereby triggers GAP activity of FLCN:FNIP2 toward RagC. We present the 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.

Rag GTPases (Rags) 将 mTORC1 募集至溶酶体膜以响应营养物质，然后在响应能量和生长因子的可用性时被激活。溶酶体滤泡素 (FLCN) 复合物 (LFC) 由无活性的 Rag 二聚体、五聚体支架 Ragulator 和 FLCN:FNIP2（FLCN 相互作用蛋白 2）GTP 酶激活蛋白 (GAP) 复合物组成，并在氨基酸过程中防止 Rag 二聚体激活饥饿。 LFC 在重新饲喂氨基酸时如何分解是一个悬而未决的问题。在这里，我们发现人溶酶体溶质载体家族 38 成员 9 (SLC38A9) 的细胞质尾部使 LFC 不稳定，从而触发 FLCN:FNIP2 对 RagC 的 GAP 活性。我们展示了 Rags 的冷冻电镜结构及其溶酶体锚定复合物 Ragulator 和 RagC GTP 水解前后状态下 SLC38A9 的细胞质尾部，这解释了 SLC38A9 如何破坏 LFC 的稳定性，从而促进 Rag 二聚体激活。