7PEA

cryo-EM structure of DEPTOR bound to human mTOR complex 1, overall refinement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Regulation of human mTOR complexes by DEPTOR.

Walchli, M.Berneiser, K.Mangia, F.Imseng, S.Craigie, L.M.Stuttfeld, E.Hall, M.N.Maier, T.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.70871
  • Primary Citation of Related Structures:  
    7PE7, 7PE8, 7PE9, 7PEA, 7PEB, 7PEC, 7PED

  • PubMed Abstract: 

    The vertebrate-specific DEP domain-containing mTOR interacting protein (DEPTOR), an oncoprotein or tumor suppressor, has important roles in metabolism, immunity, and cancer. It is the only protein that binds and regulates both complexes of mammalian target of rapamycin (mTOR), a central regulator of cell growth. Biochemical analysis and cryo-EM reconstructions of DEPTOR bound to human mTOR complex 1 (mTORC1) and mTORC2 reveal that both structured regions of DEPTOR, the PDZ domain and the DEP domain tandem (DEPt), are involved in mTOR interaction. The PDZ domain binds tightly with mildly activating effect, but then acts as an anchor for DEPt association that allosterically suppresses mTOR activation. The binding interfaces of the PDZ domain and DEPt also support further regulation by other signaling pathways. A separate, substrate-like mode of interaction for DEPTOR phosphorylation by mTOR complexes rationalizes inhibition of non-stimulated mTOR activity at higher DEPTOR concentrations. The multifaceted interplay between DEPTOR and mTOR provides a basis for understanding the divergent roles of DEPTOR in physiology and opens new routes for targeting the mTOR-DEPTOR interaction in disease.


  • Organizational Affiliation

    Biozentrum, University of Basel, Basel, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase mTORA [auth B],
E [auth A]
2,549Homo sapiensMutation(s): 0 
Gene Names: MTORFRAPFRAP1FRAP2RAFT1RAPT1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P42345 (Homo sapiens)
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Go to UniProtKB:  P42345
PHAROS:  P42345
GTEx:  ENSG00000198793 
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UniProt GroupP42345
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Target of rapamycin complex subunit LST8B [auth D],
F [auth C]
326Homo sapiensMutation(s): 0 
Gene Names: MLST8GBLLST8
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Find proteins for Q9BVC4 (Homo sapiens)
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PHAROS:  Q9BVC4
GTEx:  ENSG00000167965 
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UniProt GroupQ9BVC4
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory-associated protein of mTORC [auth F],
G [auth E]
1,396Homo sapiensMutation(s): 0 
Gene Names: RPTORKIAA1303RAPTOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N122 (Homo sapiens)
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PHAROS:  Q8N122
GTEx:  ENSG00000141564 
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UniProt GroupQ8N122
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DEP domain-containing mTOR-interacting proteinD [auth J],
H [auth I]
409Homo sapiensMutation(s): 2 
Gene Names: DEPTORDEPDC6
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Find proteins for Q8TB45 (Homo sapiens)
Explore Q8TB45 
Go to UniProtKB:  Q8TB45
PHAROS:  Q8TB45
GTEx:  ENSG00000155792 
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UniProt GroupQ8TB45
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2.0
MODEL REFINEMENTPHENIX1.19-4092

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland179323

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-08
    Type: Initial release
  • Version 1.1: 2021-09-29
    Changes: Data collection, Database references
  • Version 1.2: 2024-07-17
    Changes: Data collection, Refinement description