9ED6 | pdb_00009ed6

CryoEM map of the mLST8-Rag-Ragultor subcomplex

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): Yes 

  • Deposited: 2024-11-15 Released: 2025-09-10 
  • Deposition Author(s): Cui, Z., Hurley, J.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.98 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

Structural basis for mTORC1 activation on the lysosomal membrane.

Cui, Z.Esposito, A.Napolitano, G.Ballabio, A.Hurley, J.H.

(2025) Nature 

  • DOI: https://doi.org/10.1038/s41586-025-09545-3
  • Primary Citation of Related Structures:  
    9ED4, 9ED6, 9ED7, 9ED8

  • PubMed Abstract: 

    The mechanistic target of rapamycin complex 1 (mTORC1) integrates growth factor (GF) and nutrient signals to stimulate anabolic processes connected to cell growth and inhibit catabolic processes such as autophagy 1,2 . GF signalling through the tuberous sclerosis complex regulates the lysosomally localized small GTPase RAS homologue enriched in brain (RHEB) 3 . Direct binding of RHEB-GTP to the mTOR kinase subunit of mTORC1 allosterically activates the kinase by inducing a large-scale conformational change 4 . Here we reconstituted mTORC1 activation on membranes by RHEB, RAGs and Ragulator. Cryo-electron microscopy showed that RAPTOR and mTOR interact directly with the membrane. Full engagement of the membrane anchors is required for optimal alignment of the catalytic residues in the mTOR kinase active site. Converging signals from GFs and nutrients drive mTORC1 recruitment to and activation on lysosomal membrane in a four-step process, consisting of (1) RAG-Ragulator-driven recruitment to within ~100 Å of the lysosomal membrane; (2) RHEB-driven recruitment to within ~40 Å; (3) RAPTOR-membrane engagement and intermediate enzyme activation; and (4) mTOR-membrane engagement and full enzyme activation. RHEB and membrane engagement combined leads to full catalytic activation and structurally explains GF and nutrient signal integration at the lysosome.


  • Organizational Affiliation
    • Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein AA [auth B]313Homo sapiensMutation(s): 0 
Gene Names: RRAGA
EC: 3.6.5
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Find proteins for Q7L523 (Homo sapiens)
Explore Q7L523 
Go to UniProtKB:  Q7L523
PHAROS:  Q7L523
GTEx:  ENSG00000155876 
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UniProt GroupQ7L523
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR2B [auth E]125Homo sapiensMutation(s): 0 
Gene Names: LAMTOR2MAPBPIPROBLD3HSPC003
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Find proteins for Q9Y2Q5 (Homo sapiens)
Explore Q9Y2Q5 
Go to UniProtKB:  Q9Y2Q5
PHAROS:  Q9Y2Q5
GTEx:  ENSG00000116586 
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UniProt GroupQ9Y2Q5
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR3C [auth F]124Homo sapiensMutation(s): 0 
Gene Names: LAMTOR3MAP2K1IP1MAPKSP1PRO2783
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Find proteins for Q9UHA4 (Homo sapiens)
Explore Q9UHA4 
Go to UniProtKB:  Q9UHA4
PHAROS:  Q9UHA4
GTEx:  ENSG00000109270 
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UniProt GroupQ9UHA4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR5D [auth H]91Homo sapiensMutation(s): 0 
Gene Names: LAMTOR5HBXIPXIP
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Find proteins for O43504 (Homo sapiens)
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PHAROS:  O43504
GTEx:  ENSG00000134248 
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UniProt GroupO43504
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Target of rapamycin complex subunit LST8E [auth I]326Homo sapiensMutation(s): 0 
Gene Names: MLST8GBLLST8
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Find proteins for Q9BVC4 (Homo sapiens)
Explore Q9BVC4 
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PHAROS:  Q9BVC4
GTEx:  ENSG00000167965 
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UniProt GroupQ9BVC4
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein CF [auth C]399Homo sapiensMutation(s): 1 
Gene Names: RRAGC
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HB90 (Homo sapiens)
Explore Q9HB90 
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PHAROS:  Q9HB90
GTEx:  ENSG00000116954 
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UniProt GroupQ9HB90
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR1G [auth D]161Homo sapiensMutation(s): 0 
Gene Names: LAMTOR1C11orf59PDROPP7157
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Find proteins for Q6IAA8 (Homo sapiens)
Explore Q6IAA8 
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PHAROS:  Q6IAA8
GTEx:  ENSG00000149357 
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UniProt GroupQ6IAA8
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR4H [auth G]99Homo sapiensMutation(s): 0 
Gene Names: LAMTOR4C7orf59
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Find proteins for Q0VGL1 (Homo sapiens)
Explore Q0VGL1 
Go to UniProtKB:  Q0VGL1
PHAROS:  Q0VGL1
GTEx:  ENSG00000188186 
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UniProt GroupQ0VGL1
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesCA285366

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2025-10-01
    Changes: Data collection, Database references