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Yorodumi- EMDB-26861: A composite cryo-EM map of the mTORC1-TFEB-Rag-Ragulator complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26861 | |||||||||
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Title | A composite cryo-EM map of the mTORC1-TFEB-Rag-Ragulator complex | |||||||||
Map data | A composite map of the symmetric mTORC1-Rag-Ragulator complex | |||||||||
Sample |
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Keywords | mTORC1 / TFEB / Lysosome biogenesis / Autophagy / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information 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 / positive regulation of cytoplasmic translational initiation ...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 / positive regulation of cytoplasmic translational initiation / positive regulation of pentose-phosphate shunt / RNA polymerase III type 1 promoter sequence-specific DNA binding / RNA polymerase III type 2 promoter sequence-specific DNA binding / T-helper 1 cell lineage commitment / regulation of locomotor rhythm / positive regulation of wound healing, spreading of epidermal cells / antibacterial innate immune response / cellular response to leucine starvation / regulation of TORC1 signaling / regulation of membrane permeability / heart valve morphogenesis / TFIIIC-class transcription factor complex binding / negative regulation of lysosome organization / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC2 complex / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / protein localization to lysosome / regulation of autophagosome assembly / calcineurin-NFAT signaling cascade / nucleus localization / TORC1 signaling / voluntary musculoskeletal movement / positive regulation of odontoblast differentiation / regulation of osteoclast differentiation / regulation of TOR signaling / positive regulation of keratinocyte migration / endosome organization / cellular response to L-leucine / MTOR signalling / Amino acids regulate mTORC1 / fibroblast migration / cellular response to nutrient / lysosome localization / energy reserve metabolic process / Energy dependent regulation of mTOR by LKB1-AMPK / negative regulation of cell size / ruffle organization / protein serine/threonine kinase inhibitor activity / protein localization to membrane / kinase activator activity / positive regulation of osteoclast differentiation / cellular response to osmotic stress / enzyme-substrate adaptor activity / negative regulation of protein localization to nucleus / anoikis / cardiac muscle cell development / positive regulation of transcription by RNA polymerase III / negative regulation of calcineurin-NFAT signaling cascade / regulation of myelination / azurophil granule membrane / endosomal transport / regulation of cell size / Macroautophagy / positive regulation of oligodendrocyte differentiation / small GTPase-mediated signal transduction / negative regulation of macroautophagy / lysosome organization / positive regulation of actin filament polymerization / positive regulation of myotube differentiation / protein kinase activator activity / RHOJ GTPase cycle / behavioral response to pain / RHOQ GTPase cycle / oligodendrocyte differentiation / mTORC1-mediated signalling / Constitutive Signaling by AKT1 E17K in Cancer / germ cell development / CD28 dependent PI3K/Akt signaling / cellular response to nutrient levels / positive regulation of phosphoprotein phosphatase activity / social behavior / tertiary granule membrane / CDC42 GTPase cycle / RHOH GTPase cycle / humoral immune response / ficolin-1-rich granule membrane / HSF1-dependent transactivation / RHOG GTPase cycle / TOR signaling / positive regulation of TOR signaling / regulation of receptor recycling / neuronal action potential / RAC2 GTPase cycle / embryonic placenta development / RAC3 GTPase cycle / positive regulation of translational initiation / regulation of macroautophagy / response to amino acid / positive regulation of G1/S transition of mitotic cell cycle Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Cui Z / Hurley J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nature / Year: 2023 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 | emd_26861.map.gz | 700.5 MB | EMDB map data format | |
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Header (meta data) | emd-26861-v30.xml emd-26861.xml | 27.7 KB 27.7 KB | Display Display | EMDB header |
Images | emd_26861.png | 92.2 KB | ||
Filedesc metadata | emd-26861.cif.gz | 9.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26861 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26861 | HTTPS FTP |
-Validation report
Summary document | emd_26861_validation.pdf.gz | 534.7 KB | Display | EMDB validaton report |
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Full document | emd_26861_full_validation.pdf.gz | 534.3 KB | Display | |
Data in XML | emd_26861_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | emd_26861_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26861 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26861 | HTTPS FTP |
-Related structure data
Related structure data | 7uxhMC 7ux2C 7uxcC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26861.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
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 |
-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 |