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- PDB-7pqh: Cryo-EM structure of Saccharomyces cerevisiae TOROID (TORC1 Organ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7pqh | |||||||||||||||
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Title | Cryo-EM structure of Saccharomyces cerevisiae TOROID (TORC1 Organized in Inhibited Domains). | |||||||||||||||
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Function / homology | ![]() PIP3 activates AKT signaling / CD28 dependent PI3K/Akt signaling / regulation of snRNA pseudouridine synthesis / mitochondria-nucleus signaling pathway / Regulation of TP53 Degradation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
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![]() | Felix, J. / Prouteau, M. / Bourgoint, C. / Bonadei, L. / Desfosses, A. / Gabus, C. / Sadian, Y. / Savvides, S.N. / Gutsche, I. / Loewith, R. | |||||||||||||||
Funding support | European Union, 4items
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![]() | ![]() Title: EGOC inhibits TOROID polymerization by structurally activating TORC1. Authors: Manoël Prouteau / Clélia Bourgoint / Jan Felix / Lenny Bonadei / Yashar Sadian / Caroline Gabus / Savvas N Savvides / Irina Gutsche / Ambroise Desfosses / Robbie Loewith / ![]() ![]() ![]() Abstract: Target of rapamycin complex 1 (TORC1) is a protein kinase controlling cell homeostasis and growth in response to nutrients and stresses. In Saccharomyces cerevisiae, glucose depletion triggers a ...Target of rapamycin complex 1 (TORC1) is a protein kinase controlling cell homeostasis and growth in response to nutrients and stresses. In Saccharomyces cerevisiae, glucose depletion triggers a redistribution of TORC1 from a dispersed localization over the vacuole surface into a large, inactive condensate called TOROID (TORC1 organized in inhibited domains). However, the mechanisms governing this transition have been unclear. Here, we show that acute depletion and repletion of EGO complex (EGOC) activity is sufficient to control TOROID distribution, independently of other nutrient-signaling pathways. The 3.9-Å-resolution structure of TORC1 from TOROID cryo-EM data together with interrogation of key interactions in vivo provide structural insights into TORC1-TORC1' and TORC1-EGOC interaction interfaces. These data support a model in which glucose-dependent activation of EGOC triggers binding to TORC1 at an interface required for TOROID assembly, preventing TORC1 polymerization and promoting release of active TORC1. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 2.2 MB | Display | ![]() |
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PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 13594MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 183594.562 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: S. cerevisiae TOROIDS (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873) Lst8, P41318) and Tor2 (P32600),S. cerevisiae TOROIDS (TORC1 Organized in Inhibited ...Details: S. cerevisiae TOROIDS (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873) Lst8, P41318) and Tor2 (P32600),S. cerevisiae TOROIDS (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873) Lst8, P41318) and Tor2 (P32600) Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: KOG1, LAS24, YHR186C, H9998.14 / Production host: ![]() ![]() ![]() #2: Protein | ![]() Mass: 34077.879 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: S. cerevisiae TOROIDs (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873), Lst8 (P41318) and Tor2 (P32600) Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: LST8, YNL006W, N2005 / Production host: ![]() ![]() ![]() #3: Protein | Mass: 281915.438 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: S. cerevisiae TOROIDs (TORC1 Organized in Inhibited Domains) in the sample are composed of Kog1 (P38873), Lst8 (P41318) and Tor2 (P32600) Source: (gene. exp.) ![]() ![]() ![]() Strain: ATCC 204508 / S288c / Gene: TOR2, DRR2, TSC14, YKL203C / Production host: ![]() ![]() ![]() References: UniProt: P32600, ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: ![]() |
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Sample preparation
Component | Name: TORC1 Organized in Inhibited Domains (TOROID) / Type: COMPLEX / Entity ID: all / Source: NATURAL | ||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() ![]() Strain: RL174-5b: MATa; TB50, KOG1::TAP-HIS3 tor1Delta::KanMX6 | ||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.02 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid type: PELCO Ultrathin Carbon with Lacey Carbon | ||||||||||||||||||||||||||||||||||||||||
Vitrification![]() | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: OTHER / Nominal magnification: 37000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs![]() |
Image recording | Average exposure time: 8 sec. / Electron dose: 20 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 4901 |
Image scans | Movie frames/image: 16 / Used frames/image: 2-16 |
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Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 219455 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 218872 Details: Based on an initial helical reconstruction in RELION2.0, we performed signal subtraction to generate a set of 219,455 subtracted particles containing one isolated Torc1 assembly per segment. ...Details: Based on an initial helical reconstruction in RELION2.0, we performed signal subtraction to generate a set of 219,455 subtracted particles containing one isolated Torc1 assembly per segment. Next, we employed the localrec module in Scipion to crop and re-center the signal subtracted particles in a smaller box of 300 pixels, as well as assigning to each particle a refined defocus based on the helical geometry. Single-particle analysis of the subtracted particles using 3D refinement in RELION2.0, while imposing D1 symmetry, resulted in a map with a resolution of 4.5 Angstrom (FSC = 0.143). We then imported the particles from the RELION2.0 refinement in cryoSPARC 3.01. After 2D classification and class selection, a set of 213808 selected particles was used for Non-Uniform refinement in cryoSPARC 3.01, employing a dynamic mask, imposing D1 symmetry, using the option to keep particles from the same helix in the same half-set, and allowing high-order aberration estimation and correction, which resulted in a final map with a resolution of 3.87 Angstrom (FSC = 0.143). Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER Details: Initial homology models of Tor2 and Lst8 were generated using Phyre2, while a model of Kog1 was generated using ITasser. Homology models of Tor2, Lst8 and Kog1 were first manually placed in ...Details: Initial homology models of Tor2 and Lst8 were generated using Phyre2, while a model of Kog1 was generated using ITasser. Homology models of Tor2, Lst8 and Kog1 were first manually placed in the final 3D map followed by rigid-body fitting in Chimera. The rigid-body fitted models were subsequently subjected to a round of flexible fitting using Imodfit followed by automatic molecular dynamics flexible fitting using NAMDINATOR. The flexibly fitted structure was then refined using the Phenix software package. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 121.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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