{"doi":"10.1101/2022.09.12.507619","title":"Structural basis for mTORC1-dependent regulation of the lysosomal and autophagic transcription factor TFEB","abstract":"Abstract The transcription factor TFEB is a master regulator of lysosomal biogenesis and autophagy. The phosphorylation of TFEB by the mechanistic target of rapamycin complex 1 (mTORC1) is unique in its mTORC1 substrate recruitment mechanism, which is strictly dependent on the amino-acid-mediated activation of the RagC GAP FLCN. TFEB lacks the TOR signaling (TOS) motif responsible for the recruitment of other mTORC1 substrates. We used cryo-electron microscopy (cryo-EM) to determine the structure of TFEB as presented to mTORC1 for phosphorylation. Two full Rag-Ragulator complexes present each molecule of TFEB to the mTOR active site. One Rag-Ragulator complex is bound to Raptor in the canonical mode seen previously in the absence of TFEB. A second Rag-Ragulator complex (non-canonical) docks onto the first via a RagC GDP-dependent contact with the second Ragulator complex. The non-canonical Rag dimer binds the first helix of TFEB in a RagC GDP -dependent aspartate clamp in the cleft between the Rag G domains. Mutation of the clamp drives TFEB constitutively into the nucleus whilst having no effect on mTORC1 localization. The remainder of the 108-amino acid TFEB docking domain winds around Raptor and then back to RagA. This structure presents the phosphorylatable Ser residues of TFEB to the mTORC1 active site in a suitable geometry for their phosphorylation. The double use of RagC GDP contacts in both Rag dimers explains the strong dependence of TFEB phosphorylation on FLCN and the RagC GDP state.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":311407,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9496,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":233317,"name":"Gennaro Napolitano","orcid":"0000-0002-8615-4654","position":1,"is_corresponding":false},{"id":233320,"name":"Mariana E. G. de Araújo","orcid":"0000-0003-0576-2680","position":2,"is_corresponding":false},{"id":233319,"name":"Alessandra Esposito","orcid":"0000-0002-3838-7242","position":3,"is_corresponding":false},{"id":233330,"name":"Jlenia Monfregola","orcid":"0000-0001-7408-4428","position":4,"is_corresponding":false},{"id":233333,"name":"Lukas A. Huber","orcid":"0000-0003-1116-2120","position":5,"is_corresponding":false},{"id":233334,"name":"Andrea Ballabio","orcid":"0000-0003-1381-4604","position":6,"is_corresponding":false},{"id":237133,"name":"James H. Hurley","orcid":"0000-0001-5054-5445","position":7,"is_corresponding":false},{"id":432228,"name":"Zhicheng Cui","orcid":"0000-0003-2398-9344","position":0,"is_corresponding":true}],"reference_count":56,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:33:28.480200Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}