7OWG

human DEPTOR in a complex with mutant human mTORC1 A1459P


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Bipartite binding and partial inhibition links DEPTOR and mTOR in a mutually antagonistic embrace.

Heimhalt, M.Berndt, A.Wagstaff, J.Anandapadamanaban, M.Perisic, O.Maslen, S.McLaughlin, S.Yu, C.W.Masson, G.R.Boland, A.Ni, X.Yamashita, K.Murshudov, G.N.Skehel, M.Freund, S.M.Williams, R.L.

(2021) Elife 10

  • DOI: 10.7554/eLife.68799
  • Primary Citation of Related Structures:  
    7OWG

  • PubMed Abstract: 
  • The mTORC1 kinase complex regulates cell growth, proliferation, and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted mTORC1 with DEPTOR to understand its function. We find that DEPTOR is a unique partial mTORC1 inhibitor that may have evolved to preserve feedback inhibition of PI3K ...

    The mTORC1 kinase complex regulates cell growth, proliferation, and survival. Because mis-regulation of DEPTOR, an endogenous mTORC1 inhibitor, is associated with some cancers, we reconstituted mTORC1 with DEPTOR to understand its function. We find that DEPTOR is a unique partial mTORC1 inhibitor that may have evolved to preserve feedback inhibition of PI3K. Counterintuitively, mTORC1 activated by RHEB or oncogenic mutation is much more potently inhibited by DEPTOR. Although DEPTOR partially inhibits mTORC1, mTORC1 prevents this inhibition by phosphorylating DEPTOR, a mutual antagonism that requires no exogenous factors. Structural analyses of the mTORC1/DEPTOR complex showed DEPTOR's PDZ domain interacting with the mTOR FAT region, and the unstructured linker preceding the PDZ binding to the mTOR FRB domain. The linker and PDZ form the minimal inhibitory unit, but the N-terminal tandem DEP domains also significantly contribute to inhibition.


    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase mTORA [auth B]2,549Homo sapiensMutation(s): 1 
Gene Names: MTORFRAPFRAP1FRAP2RAFT1RAPT1mMTOR
EC: 2.7.11.1
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Find proteins for P42345 (Homo sapiens)
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PHAROS:  P42345
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UniProt GroupP42345
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Target of rapamycin complex subunit LST8B [auth E]326Homo sapiensMutation(s): 0 
Gene Names: MLST8GBLLST8
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Find proteins for Q9BVC4 (Homo sapiens)
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PHAROS:  Q9BVC4
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UniProt GroupQ9BVC4
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DEP domain-containing mTOR-interacting proteinC [auth O]409Homo sapiensMutation(s): 2 
Gene Names: DEPTORDEPDC6
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Find proteins for Q8TB45 (Homo sapiens)
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PHAROS:  Q8TB45
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Regulatory-associated protein of mTORD [auth Y]1,335Homo sapiensMutation(s): 0 
Gene Names: RPTORKIAA1303RAPTOR
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Find proteins for Q8N122 (Homo sapiens)
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PHAROS:  Q8N122
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_U105184308
Cancer Research UKUnited KingdomC14801/A21211
European Molecular Biology Organization (EMBO)United KingdomEMBO ALTF 603-2019

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-08
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references, Derived calculations