9F44

cryo-EM structure of LST2 TOS peptide bound to human mTOR complex 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

mTORC1 phosphorylates and stabilizes LST2 to negatively regulate EGFR.

Battaglioni, S.Craigie, L.M.Filippini, S.Maier, T.Hall, M.N.

(2024) Proc Natl Acad Sci U S A 121: e2405959121-e2405959121

  • DOI: https://doi.org/10.1073/pnas.2405959121
  • Primary Citation of Related Structures:  
    9F42, 9F43, 9F44, 9F45

  • PubMed Abstract: 

    TORC1 (target of rapamycin complex 1) is a highly conserved protein kinase that plays a central role in regulating cell growth. Given the role of mammalian TORC1 (mTORC1) in metabolism and disease, understanding mTORC1 downstream signaling and feedback loops is important. mTORC1 recognizes some of its substrates via a five amino acid binding sequence called the TOR signaling (TOS) motif. mTORC1 binding to a TOS motif facilitates phosphorylation of a distinct, distal site. Here, we show that LST2, also known as ZFYVE28, contains a TOS motif (amino acids 401 to 405) and is directly phosphorylated by mTORC1 at serine 670 (S670). mTORC1-mediated S670 phosphorylation promotes LST2 monoubiquitination on lysine 87 (K87). Monoubiquitinated LST2 is stable and displays a broad reticular distribution. When mTORC1 is inactive, unphosphorylated LST2 is degraded by the proteasome. The absence of LST2 enhances EGFR (epidermal growth factor receptor) signaling. We propose that mTORC1 negatively feeds back on its upstream receptor EGFR via LST2.


  • Organizational Affiliation

    Biozentrum, University of Basel, Basel 4056, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase mTOR
A, B
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)
Explore P42345 
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 LST8
C, D
326Homo sapiensMutation(s): 0 
Gene Names: MLST8GBLLST8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVC4 (Homo sapiens)
Explore Q9BVC4 
Go to UniProtKB:  Q9BVC4
PHAROS:  Q9BVC4
GTEx:  ENSG00000167965 
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UniProt GroupQ9BVC4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory-associated protein of mTOR
E, F
1,363Homo sapiensMutation(s): 0 
Gene Names: RPTORKIAA1303RAPTOR
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N122 (Homo sapiens)
Explore Q8N122 
Go to UniProtKB:  Q8N122
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
Lateral signaling target protein 2 homolog
G, H
13Homo sapiensMutation(s): 0 
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Find proteins for Q9HCC9 (Homo sapiens)
Explore Q9HCC9 
Go to UniProtKB:  Q9HCC9
PHAROS:  Q9HCC9
GTEx:  ENSG00000159733 
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UniProt GroupQ9HCC9
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.68 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland179323
H2020 Marie Curie Actions of the European CommissionEuropean Union812830

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-08-28
    Changes: Data collection, Database references