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- EMDB-26861: A composite cryo-EM map of the mTORC1-TFEB-Rag-Ragulator complex -
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Open data
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Basic information
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Title | A composite cryo-EM map of the mTORC1-TFEB-Rag-Ragulator complex | |||||||||
![]() | A composite map of the symmetric mTORC1-Rag-Ragulator complex | |||||||||
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![]() | mTORC1 / TFEB / Lysosome biogenesis / Autophagy / SIGNALING PROTEIN | |||||||||
Function / homology | ![]() regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex / regulation of cholesterol efflux / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / RNA polymerase III type 2 promoter sequence-specific DNA binding ...regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / Gtr1-Gtr2 GTPase complex / regulation of cholesterol efflux / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / RNA polymerase III type 2 promoter sequence-specific DNA binding / RNA polymerase III type 1 promoter sequence-specific DNA binding / positive regulation of cytoplasmic translational initiation / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / antibacterial innate immune response / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / TORC2 complex / regulation of membrane permeability / heart valve morphogenesis / regulation of TORC1 signaling / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / TORC1 complex / protein localization to lysosome / calcineurin-NFAT signaling cascade / nucleus localization / cellular response to methionine / voluntary musculoskeletal movement / regulation of osteoclast differentiation / regulation of TOR signaling / positive regulation of odontoblast differentiation / TORC1 signaling / positive regulation of keratinocyte migration / endosome organization / fibroblast migration / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / lysosome localization / cellular response to nutrient / regulation of autophagosome assembly / Energy dependent regulation of mTOR by LKB1-AMPK / energy reserve metabolic process / negative regulation of cell size / ruffle organization / kinase activator activity / protein localization to membrane / protein serine/threonine kinase inhibitor activity / positive regulation of osteoclast differentiation / cellular response to osmotic stress / negative regulation of protein localization to nucleus / enzyme-substrate adaptor activity / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / endosomal transport / embryonic placenta development / azurophil granule membrane / negative regulation of macroautophagy / regulation of cell size / small GTPase-mediated signal transduction / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of oligodendrocyte differentiation / Macroautophagy / positive regulation of actin filament polymerization / lysosome organization / positive regulation of myotube differentiation / protein kinase activator activity / RHOJ GTPase cycle / oligodendrocyte differentiation / behavioral response to pain / RHOQ GTPase cycle / Constitutive Signaling by AKT1 E17K in Cancer / germ cell development / mTORC1-mediated signalling / CD28 dependent PI3K/Akt signaling / : / tertiary granule membrane / CDC42 GTPase cycle / social behavior / humoral immune response / RHOH GTPase cycle / ficolin-1-rich granule membrane / HSF1-dependent transactivation / neuronal action potential / RHOG GTPase cycle / Transcriptional and post-translational regulation of MITF-M expression and activity / TOR signaling / regulation of receptor recycling / positive regulation of TOR signaling / RAC2 GTPase cycle / RAC3 GTPase cycle / response to amino acid / endomembrane system Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
![]() | Cui Z / Hurley J | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the lysosomal mTORC1-TFEB-Rag-Ragulator megacomplex. Authors: Zhicheng Cui / Gennaro Napolitano / Mariana E G de Araujo / Alessandra Esposito / Jlenia Monfregola / Lukas A Huber / Andrea Ballabio / James H Hurley / ![]() ![]() ![]() 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 ...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'. 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 through a RagC GDP-dependent contact with the second Ragulator complex. The non-canonical Rag dimer binds the first helix of TFEB with a RagC-dependent aspartate clamp in the cleft between the Rag G domains. In cellulo mutation of the clamp drives TFEB constitutively into the nucleus while having no effect on mTORC1 localization. The remainder of the 108-amino acid TFEB docking domain winds around Raptor and then back to RagA. 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. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 700.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 27.7 KB 27.7 KB | Display Display | ![]() |
Images | ![]() | 92.2 KB | ||
Filedesc metadata | ![]() | 9.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uxhMC ![]() 7ux2C ![]() 7uxcC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | A composite map of the symmetric mTORC1-Rag-Ragulator complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : The mTORC1-TFEB-Rag-Ragulator complex
+Supramolecule #1: The mTORC1-TFEB-Rag-Ragulator complex
+Macromolecule #1: Serine/threonine-protein kinase mTOR
+Macromolecule #2: Target of rapamycin complex subunit LST8
+Macromolecule #3: Regulatory-associated protein of mTOR
+Macromolecule #4: Ras-related GTP-binding protein A
+Macromolecule #5: Ras-related GTP-binding protein C
+Macromolecule #6: Ragulator complex protein LAMTOR1
+Macromolecule #7: Ragulator complex protein LAMTOR2
+Macromolecule #8: Ragulator complex protein LAMTOR3
+Macromolecule #9: Ragulator complex protein LAMTOR4
+Macromolecule #10: Ragulator complex protein LAMTOR5
+Macromolecule #11: Transcription factor EB
+Macromolecule #12: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #13: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #14: MAGNESIUM ION
+Macromolecule #15: GUANOSINE-5'-DIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL / In silico model: ab-initio reconstruction by cryoSPARC |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 192332 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |