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Yorodumi- EMDB-3814: TORC1 Organised in Inhibited Domains (TOROIDs) regulate TORC1 activity -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3814 | |||||||||||||||
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Title | TORC1 Organised in Inhibited Domains (TOROIDs) regulate TORC1 activity | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 27.0 Å | |||||||||||||||
Authors | Prouteau M / Desfosses A / Sieben C / Bourgoint C / Mozaffri NL / Demurtas D / Mitra AK / Guichard P / Manley S / Loewith R | |||||||||||||||
Funding support | Switzerland, 4 items
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Citation | Journal: Nature / Year: 2017 Title: TORC1 organized in inhibited domains (TOROIDs) regulate TORC1 activity. Authors: Manoël Prouteau / Ambroise Desfosses / Christian Sieben / Clélia Bourgoint / Nour Lydia Mozaffari / Davide Demurtas / Alok K Mitra / Paul Guichard / Suliana Manley / Robbie Loewith / Abstract: The target of rapamycin (TOR) is a eukaryotic serine/threonine protein kinase that functions in two distinct complexes, TORC1 and TORC2, to regulate growth and metabolism. GTPases, responding to ...The target of rapamycin (TOR) is a eukaryotic serine/threonine protein kinase that functions in two distinct complexes, TORC1 and TORC2, to regulate growth and metabolism. GTPases, responding to signals generated by abiotic stressors, nutrients, and, in metazoans, growth factors, play an important but poorly understood role in TORC1 regulation. Here we report that, in budding yeast, glucose withdrawal (which leads to an acute loss of TORC1 kinase activity) triggers a similarly rapid Rag GTPase-dependent redistribution of TORC1 from being semi-uniform around the vacuolar membrane to a single, vacuole-associated cylindrical structure visible by super-resolution optical microscopy. Three-dimensional reconstructions of cryo-electron micrograph images of these purified cylinders demonstrate that TORC1 oligomerizes into a higher-level hollow helical assembly, which we name a TOROID (TORC1 organized in inhibited domain). Fitting of the recently described mammalian TORC1 structure into our helical map reveals that oligomerization leads to steric occlusion of the active site. Guided by the implications from our reconstruction, we present a TOR1 allele that prevents both TOROID formation and TORC1 inactivation in response to glucose withdrawal, demonstrating that oligomerization is necessary for TORC1 inactivation. Our results reveal a novel mechanism by which Rag GTPases regulate TORC1 activity and suggest that the reversible assembly and/or disassembly of higher-level structures may be an underappreciated mechanism for the regulation of protein kinases. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3814.map.gz | 9.6 MB | EMDB map data format | |
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Header (meta data) | emd-3814-v30.xml emd-3814.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | emd_3814.png | 243.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3814 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3814 | HTTPS FTP |
-Validation report
Summary document | emd_3814_validation.pdf.gz | 234.8 KB | Display | EMDB validaton report |
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Full document | emd_3814_full_validation.pdf.gz | 233.9 KB | Display | |
Data in XML | emd_3814_validation.xml.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3814 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3814 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3814.map.gz / Format: CCP4 / Size: 13.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 4.52 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Helical assembly of yeast Target of Rapamycin Complex 1 (TORC1)
Entire | Name: Helical assembly of yeast Target of Rapamycin Complex 1 (TORC1) |
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Components |
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-Supramolecule #1: Helical assembly of yeast Target of Rapamycin Complex 1 (TORC1)
Supramolecule | Name: Helical assembly of yeast Target of Rapamycin Complex 1 (TORC1) type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | helical array |
-Sample preparation
Buffer | pH: 6 |
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Vitrification | Cryogen name: PROPANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 24.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |