7PQH

Cryo-EM structure of Saccharomyces cerevisiae TOROID (TORC1 Organized in Inhibited Domains).


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

EGOC inhibits TOROID polymerization by structurally activating TORC1.

Prouteau, M.Bourgoint, C.Felix, J.Bonadei, L.Sadian, Y.Gabus, C.Savvides, S.N.Gutsche, I.Desfosses, A.Loewith, R.

(2023) Nat Struct Mol Biol 30: 273-285

  • DOI: https://doi.org/10.1038/s41594-022-00912-6
  • Primary Citation of Related Structures:  
    7PQH

  • PubMed 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 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.


  • Organizational Affiliation

    Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland. manoel.prouteau@unige.ch.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Target of rapamycin complex 1 subunit KOG1,Target of rapamycin complex 1 subunit Kog1
A, B, G, J
1,608Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: KOG1LAS24YHR186CH9998.14
UniProt
Find proteins for P38873 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38873 
Go to UniProtKB:  P38873
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38873
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Target of rapamycin complex subunit LST8
C, D, I, L
303Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: LST8YNL006WN2005
UniProt
Find proteins for P41318 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41318 
Go to UniProtKB:  P41318
Entity Groups  
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UniProt GroupP41318
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase TOR2
E, F, H, K
2,474Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOR2DRR2TSC14YKL203C
EC: 2.7.1.67 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt
Find proteins for P32600 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32600 
Go to UniProtKB:  P32600
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32600
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.87 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3.01

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union834394
Swiss National Science FoundationEuropean Union179517
H2020 Marie Curie Actions of the European CommissionEuropean Union789385
European Research Council (ERC)European Union64778

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2023-02-08
    Changes: Database references
  • Version 1.2: 2023-03-29
    Changes: Database references