7PEB

cryo-EM structure of DEPTOR bound to human mTOR complex 1, focussed on one protomer

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 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

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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase mTOR2,549Homo sapiensMutation(s): 0 
Gene Names: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1
EC: 2.7.11.1
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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 C]326Homo sapiensMutation(s): 0 
Gene Names: MLST8, GBL, LST8
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Regulatory-associated protein of mTORC [auth E]1,396Homo sapiensMutation(s): 0 
Gene Names: RPTOR, KIAA1303, RAPTOR
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DEP domain-containing mTOR-interacting proteinD [auth I]409Homo sapiensMutation(s): 2 
Gene Names: DEPTOR, DEPDC6
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Find proteins for Q8TB45 (Homo sapiens)
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP
Download Ideal Coordinates CCD File 
E [auth A]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.67 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19-4092
RECONSTRUCTIONcryoSPARC3.2.0

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