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- EMDB-3814: TORC1 Organised in Inhibited Domains (TOROIDs) regulate TORC1 activity -

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Basic information

Entry
Database: EMDB / ID: EMD-3814
TitleTORC1 Organised in Inhibited Domains (TOROIDs) regulate TORC1 activity
Map data
Sample
  • Complex: Helical assembly of yeast Target of Rapamycin Complex 1 (TORC1)
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 27.0 Å
AuthorsProuteau M / Desfosses A / Sieben C / Bourgoint C / Mozaffri NL / Demurtas D / Mitra AK / Guichard P / Manley S / Loewith R
Funding support Switzerland, 4 items
OrganizationGrant numberCountry
Swiss National Science FoundationFNS 31003A_160023 Switzerland
Swiss National Science FoundationNCCR Chemical Biology Switzerland
European Research CouncilTORCH Switzerland
Swiss National Science FoundationSystemsX Switzerland
CitationJournal: 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
DepositionJul 17, 2017-
Header (metadata) releaseAug 23, 2017-
Map releaseOct 18, 2017-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_3814.map.gz / Format: CCP4 / Size: 13.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 4.52 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-2.1915727 - 3.47464
Average (Standard dev.)0.012138496 (±0.63765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-140
Dimensions160160140
Spacing160160140
CellA: 723.2 Å / B: 723.2 Å / C: 632.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.524.524.52
M x/y/z160160140
origin x/y/z0.0000.0000.000
length x/y/z723.200723.200632.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-160-160-140
NC/NR/NS160160140
D min/max/mean-2.1923.4750.012

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Supplemental data

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Sample components

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Entire : Helical assembly of yeast Target of Rapamycin Complex 1 (TORC1)

EntireName: Helical assembly of yeast Target of Rapamycin Complex 1 (TORC1)
Components
  • Complex: Helical assembly of yeast Target of Rapamycin Complex 1 (TORC1)

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Supramolecule #1: Helical assembly of yeast Target of Rapamycin Complex 1 (TORC1)

SupramoleculeName: Helical assembly of yeast Target of Rapamycin Complex 1 (TORC1)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 6
VitrificationCryogen name: PROPANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 24.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 4352 / Software - Name: EMAN2 (ver. 2.11) / Software - details: e2helixboxer.py , manual picking
Details: Total length of non-overlapping segments before selection : 53.6 micrometers Number of tubules : 324
CTF correctionSoftware - Name: CTFFIND (ver. 3.5)
Startup modelType of model: OTHER / Details: Solid cylinder of 560 Angstrom in diameter
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPRING (ver. 0.83)
Final reconstructionApplied symmetry - Helical parameters - Δz: 28.1 Å
Applied symmetry - Helical parameters - Δ&Phi: 47.62 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPRING (ver. 0.83) / Number images used: 4049

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