6EMK

Cryo-EM Structure of Saccharomyces cerevisiae Target of Rapamycin Complex 2


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 Å
  • Resolution: 8.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Cryo-EM structure of Saccharomyces cerevisiae target of rapamycin complex 2.

Karuppasamy, M.Kusmider, B.Oliveira, T.M.Gaubitz, C.Prouteau, M.Loewith, R.Schaffitzel, C.

(2017) Nat Commun 8: 1729-1729

  • DOI: https://doi.org/10.1038/s41467-017-01862-0
  • Primary Citation of Related Structures:  
    6EMK

  • PubMed Abstract: 

    The target of rapamycin (TOR) kinase assembles into two distinct multiprotein complexes, conserved across eukaryote evolution. In contrast to TOR complex 1 (TORC1), TORC2 kinase activity is not inhibited by the macrolide rapamycin. Here, we present the structure of Saccharomyces cerevisiae TORC2 determined by electron cryo-microscopy. TORC2 contains six subunits assembling into a 1.4 MDa rhombohedron. Tor2 and Lst8 form the common core of both TOR complexes. Avo3/Rictor is unique to TORC2, but interacts with the same HEAT repeats of Tor2 that are engaged by Kog1/Raptor in mammalian TORC1, explaining the mutual exclusivity of these two proteins. Density, which we conclude is Avo3, occludes the FKBP12-rapamycin-binding site of Tor2's FRB domain rendering TORC2 rapamycin insensitive and recessing the kinase active site. Although mobile, Avo1/hSin1 further restricts access to the active site as its conserved-region-in-the-middle (CRIM) domain is positioned along an edge of the TORC2 active-site-cleft, consistent with a role for CRIM in substrate recruitment.


  • Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042, Grenoble, France.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase TOR2
A, C
2,474Saccharomyces cerevisiae S288CMutation(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))
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Go to UniProtKB:  P32600
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UniProt GroupP32600
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Target of rapamycin complex subunit LST8
B, D
303Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LST8YNL006WN2005
UniProt
Find proteins for P41318 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P41318
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UniProt GroupP41318
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Target of rapamycin complex 2 subunit TSC11
E, F
303Saccharomyces cerevisiae S288CMutation(s): 0 
Sequence Annotations
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Target of rapamycin complex 2 subunit AVO2
G, H
426Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: AVO2YMR068WYM9916.07
UniProt
Find proteins for Q04749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupQ04749
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Target of rapamycin complex 2 subunit AVO1
I, J
1,176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: AVO1YOL078WO1110
UniProt
Find proteins for Q08236 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08236 
Go to UniProtKB:  Q08236
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UniProt GroupQ08236
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 7.90 Å
  • Resolution: 8.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4
RECONSTRUCTIONRELION1.4
MODEL REFINEMENTREFMAC5.8.0158

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationFNS 31003A_160023
Sinergia grantCRSII3_136254
European Research CouncilTORCH 614552
European Research CouncilStarting Grant, No 281331

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Refinement description
  • Version 1.2: 2019-12-11
    Changes: Other
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references, Refinement description