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Yorodumi- EMDB-26857: cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex with s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26857 | |||||||||
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Title | cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex with symmetry expansion | |||||||||
Map data | ||||||||||
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 / antibacterial innate immune response ...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 / antibacterial innate immune response / 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 / regulation of locomotor rhythm / T-helper 1 cell lineage commitment / positive regulation of pentose-phosphate shunt / positive regulation of wound healing, spreading of epidermal cells / TORC2 complex / cellular response to leucine starvation / TFIIIC-class transcription factor complex binding / regulation of TORC1 signaling / regulation of membrane permeability / negative regulation of lysosome organization / heart valve morphogenesis / nucleus localization / protein localization to lysosome / RNA polymerase III type 3 promoter sequence-specific DNA binding / TORC1 complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / regulation of TOR signaling / calcineurin-NFAT signaling cascade / voluntary musculoskeletal movement / TORC1 signaling / regulation of osteoclast differentiation / positive regulation of odontoblast differentiation / positive regulation of keratinocyte migration / endosome organization / fibroblast migration / lysosome localization / cellular response to L-leucine / Amino acids regulate mTORC1 / MTOR signalling / cellular response to nutrient / regulation of autophagosome assembly / cellular response to methionine / Energy dependent regulation of mTOR by LKB1-AMPK / energy reserve metabolic process / negative regulation of cell size / protein localization to membrane / ruffle organization / kinase activator activity / positive regulation of osteoclast differentiation / cellular response to osmotic stress / protein serine/threonine kinase inhibitor activity / 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 / azurophil granule membrane / regulation of myelination / endosomal transport / positive regulation of actin filament polymerization / small GTPase-mediated signal transduction / regulation of cell size / negative regulation of macroautophagy / positive regulation of oligodendrocyte differentiation / lysosome organization / Macroautophagy / positive regulation of myotube differentiation / protein kinase activator activity / behavioral response to pain / RHOJ GTPase cycle / RHOQ GTPase cycle / oligodendrocyte differentiation / Constitutive Signaling by AKT1 E17K in Cancer / mTORC1-mediated signalling / germ cell development / tertiary granule membrane / : / CD28 dependent PI3K/Akt signaling / social behavior / humoral immune response / CDC42 GTPase cycle / ficolin-1-rich granule membrane / RHOH GTPase cycle / HSF1-dependent transactivation / RHOG GTPase cycle / neuronal action potential / positive regulation of TOR signaling / regulation of receptor recycling / embryonic placenta development / response to amino acid / RAC2 GTPase cycle / Transcriptional and post-translational regulation of MITF-M expression and activity / TOR signaling / endomembrane system / RAC3 GTPase cycle / 'de novo' pyrimidine nucleobase biosynthetic process 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_26857.map.gz | 43.3 MB | EMDB map data format | |
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Header (meta data) | emd-26857-v30.xml emd-26857.xml | 31.2 KB 31.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26857_fsc.xml | 19.4 KB | Display | FSC data file |
Images | emd_26857.png | 86.1 KB | ||
Filedesc metadata | emd-26857.cif.gz | 9.9 KB | ||
Others | emd_26857_half_map_1.map.gz emd_26857_half_map_2.map.gz | 720.4 MB 720.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26857 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26857 | HTTPS FTP |
-Validation report
Summary document | emd_26857_validation.pdf.gz | 837.5 KB | Display | EMDB validaton report |
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Full document | emd_26857_full_validation.pdf.gz | 837.1 KB | Display | |
Data in XML | emd_26857_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | emd_26857_validation.cif.gz | 38.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26857 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26857 | HTTPS FTP |
-Related structure data
Related structure data | 7uxcMC 7ux2C 7uxhC 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_26857.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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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
-Half map: #2
File | emd_26857_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26857_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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 |