9ED4 | pdb_00009ed4

A composite map of mTORC1-Rag-Ragultor-4EBP1 on membrane


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 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
Target of rapamycin complex subunit LST8A [auth B],
M
326Homo sapiensMutation(s): 0 
Gene Names: MLST8GBLLST8
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PHAROS:  Q9BVC4
GTEx:  ENSG00000167965 
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UniProt GroupQ9BVC4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding protein RhebB [auth L],
N
184Homo sapiensMutation(s): 0 
Gene Names: RHEBRHEB2
EC: 3.6.5
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GTEx:  ENSG00000106615 
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UniProt GroupQ15382
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase mTORC [auth A],
O
2,549Homo sapiensMutation(s): 0 
Gene Names: MTORFRAPFRAP1FRAP2RAFT1RAPT1
EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (UniProt)
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GTEx:  ENSG00000198793 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein A
D, P
313Homo sapiensMutation(s): 0 
Gene Names: RRAGA
EC: 3.6.5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR2E [auth G],
Q
125Homo sapiensMutation(s): 0 
Gene Names: LAMTOR2MAPBPIPROBLD3HSPC003
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GTEx:  ENSG00000116586 
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UniProt GroupQ9Y2Q5
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR3F [auth H],
R
124Homo sapiensMutation(s): 0 
Gene Names: LAMTOR3MAP2K1IP1MAPKSP1PRO2783
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GTEx:  ENSG00000109270 
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UniProt GroupQ9UHA4
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR5G [auth J],
S
91Homo sapiensMutation(s): 0 
Gene Names: LAMTOR5HBXIPXIP
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GTEx:  ENSG00000134248 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 4E-binding protein 1H [auth K],
T
118Homo sapiensMutation(s): 0 
Gene Names: EIF4EBP1
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GTEx:  ENSG00000187840 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory-associated protein of mTORI [auth C],
U
1,335Homo sapiensMutation(s): 0 
Gene Names: RPTORKIAA1303RAPTOR
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GTEx:  ENSG00000141564 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein CJ [auth E],
V
399Homo sapiensMutation(s): 1 
Gene Names: RRAGC
EC: 3.6.5
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GTEx:  ENSG00000116954 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR1K [auth F],
W
161Homo sapiensMutation(s): 0 
Gene Names: LAMTOR1C11orf59PDROPP7157
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR4L [auth I],
X
99Homo sapiensMutation(s): 0 
Gene Names: LAMTOR4C7orf59
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GTEx:  ENSG00000188186 
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Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHP
Query on IHP

Download Ideal Coordinates CCD File 
DA [auth A],
MA [auth O]
INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
GSP
Query on GSP

Download Ideal Coordinates CCD File 
HA [auth N],
Y [auth L]
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
GTP
Query on GTP

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EA [auth D],
NA [auth P]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ANP
Query on ANP

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AA [auth A],
JA [auth O]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GDP
Query on GDP

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GA [auth E],
PA [auth V]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

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BA [auth A]
CA [auth A]
FA [auth D]
IA [auth N]
KA [auth O]
BA [auth A],
CA [auth A],
FA [auth D],
IA [auth N],
KA [auth O],
LA [auth O],
OA [auth P],
Z [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
MODEL REFINEMENTISOLDE
RECONSTRUCTIONcryoSPARC4.4

Structure Validation

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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