Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex

Cui Z, Napolitano G, de Araujo MEG, Esposito A, Monfregola J, Huber LA, Ballabio A, Hurley JH · 2023 · Nature · Atlas ID CUI2023

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 no other mTORC1 substrate does. 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

ShowHide

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

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	2026-09-23
Source	DOI 10.1038/s41586-022-05652-7 · PMID 36697823 · Free full text (PMC9931586)

Extracted findings

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

In the Atlas

Cite this paper

ShowHide

Cui, Z., Napolitano, G., de Araujo, M. E. G., Esposito, A., Monfregola, J., Huber, L. A., Ballabio, A., & Hurley, J. H. (2023). Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex. Nature. https://doi.org/10.1038/s41586-022-05652-7

@article{CUI2023,
  author       = {Cui, Z. and Napolitano, G. and de Araujo, M. E. G. and Esposito, A. and Monfregola, J. and Huber, L. A. and Ballabio, A. and Hurley, J. H.},
  title        = {{Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex}},
  journal      = {Nature},
  year         = {2023},
  doi          = {10.1038/s41586-022-05652-7},
  note         = {PMID: 36697823},
}

Cite this Atlas record

The record is the Atlas's own work — the evidence label, the extracted findings and the links. It is cited as part of the dataset, not as the paper.

Barton, O. (2026). Oliver's mTOR Atlas (record CUI2023) [Data set]. https://mtor-atlas.org/study/CUI2023/ · Dataset DOI 10.5281/zenodo.22059963

@misc{atlas_CUI2023,
  author       = {Barton, Oliver},
  title        = {{Oliver's mTOR Atlas}, record CUI2023},
  howpublished = {Data set},
  year         = {2026},
  url          = {https://mtor-atlas.org/study/CUI2023/},
  doi          = {10.5281/zenodo.22059963}
}