6U62

Raptor-Rag-Ragulator complex

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

  • Deposited: 2019-08-29 Released: 2019-10-30 
  • Deposition Author(s): Rogala, K.B., Sabatini, D.M.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Department of Defense (DOD, United States), Lustgarten Foundation, Tuberous Sclerosis Association, Howard Hughes Medical Institute (HHMI), American Cancer Society

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the docking of mTORC1 on the lysosomal surface.

Rogala, K.B.Gu, X.Kedir, J.F.Abu-Remaileh, M.Bianchi, L.F.Bottino, A.M.S.Dueholm, R.Niehaus, A.Overwijn, D.Fils, A.P.Zhou, S.X.Leary, D.Laqtom, N.N.Brignole, E.J.Sabatini, D.M.

(2019) Science 366: 468-475

  • DOI: https://doi.org/10.1126/science.aay0166
  • Primary Citation of Related Structures:  
    6U62

  • PubMed Abstract: 

    The mTORC1 (mechanistic target of rapamycin complex 1) protein kinase regulates growth in response to nutrients and growth factors. Nutrients promote its translocation to the lysosomal surface, where its Raptor subunit interacts with the Rag guanosine triphosphatase (GTPase)-Ragulator complex. Nutrients switch the heterodimeric Rag GTPases among four different nucleotide-binding states, only one of which (RagA/B•GTP-RagC/D•GDP) permits mTORC1 association. We used cryo-electron microscopy to determine the structure of the supercomplex of Raptor with Rag-Ragulator at a resolution of 3.2 angstroms. Our findings indicate that the Raptor α-solenoid directly detects the nucleotide state of RagA while the Raptor "claw" threads between the GTPase domains to detect that of RagC. Mutations that disrupted Rag-Raptor binding inhibited mTORC1 lysosomal localization and signaling. By comparison with a structure of mTORC1 bound to its activator Rheb, we developed a model of active mTORC1 docked on the lysosome.


  • Organizational Affiliation

    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory-associated protein of mTOR1,392Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein A313Homo sapiensMutation(s): 0 
Gene Names: RRAGA
UniProt & NIH Common Fund Data Resources
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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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein C400Homo sapiensMutation(s): 2 
Gene Names: RRAGC
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Find proteins for Q9HB90 (Homo sapiens)
Explore Q9HB90 
Go to UniProtKB:  Q9HB90
PHAROS:  Q9HB90
GTEx:  ENSG00000116954 
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UniProt GroupQ9HB90
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR1158Homo sapiensMutation(s): 0 
Gene Names: LAMTOR1C11orf59PDROPP7157
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Find proteins for Q6IAA8 (Homo sapiens)
Explore Q6IAA8 
Go to UniProtKB:  Q6IAA8
PHAROS:  Q6IAA8
GTEx:  ENSG00000149357 
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UniProt GroupQ6IAA8
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR2125Homo 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: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR3162Homo 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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR4100Homo 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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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR591Homo sapiensMutation(s): 0 
Gene Names: LAMTOR5HBXIPXIP
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Find proteins for O43504 (Homo sapiens)
Explore O43504 
Go to UniProtKB:  O43504
PHAROS:  O43504
GTEx:  ENSG00000134248 
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UniProt GroupO43504
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.18 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesR01 CA103866
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA129105
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR37 AI47389
Department of Defense (DOD, United States)United StatesW81XWH-07-0448
Lustgarten FoundationUnited States--
Tuberous Sclerosis AssociationUnited Kingdom--
Howard Hughes Medical Institute (HHMI)United States--
American Cancer SocietyUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-30
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references