Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex
What this study shows
First structural view of how mTORC1 actually reaches TFEB to phosphorylate it: two full Rag-Ragulator complexes present a single TFEB molecule to the mTOR active site, one in the normal Raptor-docking arrangement and a second, non-canonical one that grips TFEB's own first helix. Mutating that grip point drives TFEB straight into the nucleus (turning on autophagy/lysosome genes) without disturbing where mTORC1 itself sits. Explains, at the level of atoms, why TFEB phosphorylation needs the tumour suppressor FLCN and the GDP-loaded state of RagC in a way the authors report for no other mTORC1 substrate. Boundary: cryo-EM of a complex reconstituted from purified human proteins — a static structural snapshot, not a live cell or a real-time measurement.
Abstract
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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 GTPase activating protein FLCN. TFEB lacks the TOR signalling motif responsible for the recruitment of other mTORC1 substrates. We used cryogenic-electron microscopy to determine the structure of TFEB as presented to mTORC1 for phosphorylation, which we refer to as the 'megacomplex'.
Read the full abstract on PubMed →At a glance
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| Evidence type | M Molecular — cells, biochemistry, structure Marked M because it is molecular or in-vitro work (model: Cryo-EM structure (human proteins, cell-free reconstitution)) rather than a whole-organism health-outcome study. That is often exactly where causal biology gets established -- the code says which system the finding was shown in, and nothing about how good the work is. |
| Study type | 5 - Mechanistic / In Vitro |
| Model system | Cryo-EM structure (human proteins, cell-free reconstitution) |
| Journal | Nature |
| Year | 2023 |
| Peer reviewed | Yes |
| Record last updated | 2026-10-01 |
| Source | DOI 10.1038/s41586-022-05652-7 · PMID 36697823 · Free full text (PMC9931586) |
Where this study fits
How this study connects to the pathway map, open questions, people and other studies in the Atlas.
Pathway relations
Supports
mTORC1 inhibits TFEBStrongest evidence: M (Molecular — cells, biochemistry, structure) · settled in the literature · Status: Proposed
plausible in people, not shown directly
RagD specifically (more than RagC) promotes TFEB/TFE3 phosphorylation via tighter LAMTOR binding — GOL2022 shows this is paralogue-specific, not a generic Rag-dimer property.
People in the Atlas
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Structural biologist who solved cryo-EM structures of the mTORC1–TFEB–Rag–Ragulator megacomplex and of mTORC1 switched on by RHEB and the Rags on a lipid membrane.
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Structural biologist who uses cryo-EM to show how protein machines assembled on membranes control autophagy and nutrient signalling. His lab solved structures of the Rag–Ragulator complex and of the whole mTORC1–TFEB–Rag–Ragulator assembly on the lysosome
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mTORC1-TFEB lysosomal signalling
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Cell biologist in Lukas Huber's group in Innsbruck who solved the crystal structure of the Ragulator (LAMTOR) complex, the lysosomal platform on which mTORC1 is switched on
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Lysosomal signalling and TFEB regulation
More: 3 other authors
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TIGEM postdoc and co-author on the cryo-EM structure of the mTORC1–TFEB–Rag–Ragulator megacomplex and on the TBK1/ULK1 lysosomal stress route to TFEB.
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Cell biologist who studied the p14-MP1 scaffold on late endosomes, a complex later recognised as part of Ragulator (LAMTOR), the lysosomal platform that holds mTORC1 in place
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Discovered that the transcription factor TFEB is a master switch for building lysosomes (SAR2009) and for autophagy. His lab was one of the groups that showed in 2012 that mTORC1 keeps TFEB out of the nucleus from the lysosome surface, and later (2020) that constitutive TFEB activation drives the kidney disease of Birt-Hogg-Dubé syndrome
Related studies
- R Substrate-selective mTORC1 regulation and gene dosage-dependent tissue divergence in Birt-Hogg-Dubé syndrome
CAO2026 · 2026 · Shares: TFEB, Rag GTPases, mTORC1, FLCN / FNIP1/2
- A Synergistic role of TFEB/TFE3 and mTORC1 in kidney cystogenesis and tumorigenesis
FER2026 · 2026 · Shares: TFEB, Rag GTPases, mTORC1, FLCN / FNIP1/2
- M A Rag GTPase dimer code defines the regulation of mTORC1 by amino acids
GOL2022 · 2022 · Shares: TFEB, Rag GTPases, mTORC1, Ragulator
- M Structural basis for mTORC1 activation on the lysosomal membrane
CUI2025 · 2025 · Shares: Raptor, Rag GTPases, mTORC1, Ragulator
- M Structural basis for the docking of mTORC1 on the lysosomal surface
ROG2019 · 2019 · Shares: Raptor, Rag GTPases, mTORC1, Ragulator
More related studies
- M FLCN loss is characterized by SQSTM1/p62 accumulation despite functional autophagy flux in Birt-Hogg-Dubé syndrome-associated kidney cancer
ULL2026 · 2026 · Shares: TFEB, mTORC1, FLCN / FNIP1/2
- M A TBK1/ULK1 signalling axis couples lysosomal stress to TFEB activation.
ESP2026 · 2026 · Shares: TFEB, FLCN / FNIP1/2
- M Structure and function of TM6SF1 reveals role in mTORC1 signaling
HON2026 · 2026 · Shares: TFEB, mTORC1, Ragulator
- M MTORC1 functions as a transcriptional regulator of autophagy by preventing nuclear transport of TFEB
MAR2012 · 2012 · Shares: TFEB, mTORC1, Ragulator
- M Hybrid Structure of the RagA/C-Ragulator mTORC1 Activation Complex
SUX2017 · 2017 · Shares: Rag GTPases, mTORC1, Ragulator
- M mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H(+)-ATPase
ZON2011 · 2011 · Shares: Rag GTPases, mTORC1, Ragulator
- M Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids
SAN2010 · 2010 · Shares: Rag GTPases, mTORC1, Ragulator
- M Rag GTPases mediate amino acid-dependent recruitment of TFEB and MITF to lysosomes
MAR2013 · 2013 · Shares: TFEB, Rag GTPases, mTORC1
Topics
Extracted findings
These fields were extracted from the paper with AI assistance and have not been checked against the source. Read them as a pointer into the paper, not as curated claims; where they disagree with the curated summary above, the curated summary stands.
| Intervention | Structural (cryo-EM, reconstituted complex) |
| Target | mTORC1-TFEB-Rag-Ragulator megacomplex |
| Model | Human proteins, cell-free reconstitution |
| Effect | Structure of TFEB captured between two Rag-Ragulator complexes for mTORC1-mediated phosphorylation; non-canonical Rag dimer grips TFEB's N-terminal helix via a RagC-GDP-dependent clamp |
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