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Open data
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Basic information
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Title | Composite cryo-EM map of the Raptor-TFEB-Rag-Ragulator complex | |||||||||
![]() | A composite map of the Raptor-TFEB-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 / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / positive regulation of pentose-phosphate shunt / regulation of TORC1 signaling ...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 / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / positive regulation of pentose-phosphate shunt / regulation of TORC1 signaling / antibacterial innate immune response / TORC1 complex / protein localization to lysosome / positive regulation of odontoblast differentiation / regulation of TOR signaling / regulation of lysosome organization / fibroblast migration / MTOR signalling / Amino acids regulate mTORC1 / cellular response to L-leucine / lysosome localization / endosome organization / Energy dependent regulation of mTOR by LKB1-AMPK / TORC1 signaling / serine/threonine protein kinase complex / positive regulation of osteoclast differentiation / cellular response to osmotic stress / kinase activator activity / protein localization to membrane / azurophil granule membrane / positive regulation of transcription by RNA polymerase III / endosomal transport / lysosome organization / small GTPase-mediated signal transduction / Macroautophagy / regulation of cell size / RHOJ GTPase cycle / RHOQ GTPase cycle / TOR signaling / mTORC1-mediated signalling / humoral immune response / tertiary granule membrane / CDC42 GTPase cycle / RHOH GTPase cycle / ficolin-1-rich granule membrane / protein kinase activator activity / RHOG GTPase cycle / social behavior / protein serine/threonine kinase inhibitor activity / regulation of receptor recycling / positive regulation of TOR signaling / RAC2 GTPase cycle / HSF1-dependent transactivation / RAC3 GTPase cycle / enzyme-substrate adaptor activity / positive regulation of G1/S transition of mitotic cell cycle / response to amino acid / embryonic placenta development / positive regulation of lipid biosynthetic process / cellular response to nutrient levels / specific granule membrane / tumor necrosis factor-mediated signaling pathway / protein-membrane adaptor activity / positive regulation of endothelial cell proliferation / 14-3-3 protein binding / RAC1 GTPase cycle / positive regulation of autophagy / positive regulation of TORC1 signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / negative regulation of autophagy / RNA splicing / cellular response to amino acid starvation / viral genome replication / guanyl-nucleotide exchange factor activity / cholesterol homeostasis / cellular response to starvation / positive regulation of glycolytic process / Regulation of PTEN gene transcription / positive regulation of interleukin-8 production / TP53 Regulates Metabolic Genes / phosphoprotein binding / cellular response to amino acid stimulus / regulation of cell growth / cellular response to glucose stimulus / MAP2K and MAPK activation / small GTPase binding / autophagy / response to virus / positive regulation of protein localization to nucleus / cytoplasmic stress granule / sequence-specific double-stranded DNA binding / GDP binding / late endosome membrane / E3 ubiquitin ligases ubiquitinate target proteins / late endosome / intracellular protein localization / glucose homeostasis / GTPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / positive regulation of cell growth Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 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 | ![]() | 115.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.5 KB 23.5 KB | Display Display | ![]() |
Images | ![]() | 63.8 KB | ||
Filedesc metadata | ![]() | 7.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 493.6 KB | Display | ![]() |
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Full document | ![]() | 493.2 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 7.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ux2MC ![]() 7uxcC ![]() 7uxhC 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 Raptor-TFEB-Rag-Ragulator complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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 Raptor-TFEB-Rag-Ragulator complex
+Supramolecule #1: The Raptor-TFEB-Rag-Ragulator complex
+Macromolecule #1: Regulatory-associated protein of mTOR
+Macromolecule #2: Ras-related GTP-binding protein A
+Macromolecule #3: Ras-related GTP-binding protein C
+Macromolecule #4: Ragulator complex protein LAMTOR1
+Macromolecule #5: Ragulator complex protein LAMTOR2
+Macromolecule #6: Ragulator complex protein LAMTOR3
+Macromolecule #7: Ragulator complex protein LAMTOR4
+Macromolecule #8: Ragulator complex protein LAMTOR5
+Macromolecule #9: Transcription factor EB
+Macromolecule #10: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #11: MAGNESIUM ION
+Macromolecule #12: 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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Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 377569 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-7ux2: |