6CES

Cryo-EM structure of GATOR1-RAG

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens, Escherichia coli BL21(DE3)
  • Mutation(s): Yes 

  • Deposited: 2018-02-12 Released: 2018-03-28 
  • Deposition Author(s): Shen, K., Huang, R.K., Brignole, E.J., Yu, Z., 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), National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI), Life Sciences Research Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.8 of the entry. See complete history


Literature

Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes.

Shen, K.Huang, R.K.Brignole, E.J.Condon, K.J.Valenstein, M.L.Chantranupong, L.Bomaliyamu, A.Choe, A.Hong, C.Yu, Z.Sabatini, D.M.

(2018) Nature 556: 64-69

  • DOI: https://doi.org/10.1038/nature26158
  • Primary Citation of Related Structures:  
    6CES, 6CET

  • PubMed Abstract: 

    Nutrients, such as amino acids and glucose, signal through the Rag GTPases to activate mTORC1. The GATOR1 protein complex-comprising DEPDC5, NPRL2 and NPRL3-regulates the Rag GTPases as a GTPase-activating protein (GAP) for RAGA; loss of GATOR1 desensitizes mTORC1 signalling to nutrient starvation. GATOR1 components have no sequence homology to other proteins, so the function of GATOR1 at the molecular level is currently unknown. Here we used cryo-electron microscopy to solve structures of GATOR1 and GATOR1-Rag GTPases complexes. GATOR1 adopts an extended architecture with a cavity in the middle; NPRL2 links DEPDC5 and NPRL3, and DEPDC5 contacts the Rag GTPase heterodimer. Biochemical analyses reveal that our GATOR1-Rag GTPases structure is inhibitory, and that at least two binding modes must exist between the Rag GTPases and GATOR1. Direct interaction of DEPDC5 with RAGA inhibits GATOR1-mediated stimulation of GTP hydrolysis by RAGA, whereas weaker interactions between the NPRL2-NPRL3 heterodimer and RAGA execute GAP activity. These data reveal the structure of a component of the nutrient-sensing mTORC1 pathway and a non-canonical interaction between a GAP and its substrate GTPase.


  • Organizational Affiliation

    Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 455 Main Street, Cambridge, Massachusetts 02142, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GATOR complex protein NPRL2A [auth N]380Homo sapiensMutation(s): 0 
Gene Names: NPRL2TUSC4
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTW4 (Homo sapiens)
Explore Q8WTW4 
Go to UniProtKB:  Q8WTW4
PHAROS:  Q8WTW4
GTEx:  ENSG00000114388 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WTW4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GATOR complex protein NPRL3B [auth M]569Homo sapiensMutation(s): 0 
Gene Names: NPRL3C16orf35CGTHBAMARE
UniProt & NIH Common Fund Data Resources
Find proteins for Q12980 (Homo sapiens)
Explore Q12980 
Go to UniProtKB:  Q12980
PHAROS:  Q12980
GTEx:  ENSG00000103148 
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UniProt GroupQ12980
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GATOR complex protein DEPDC5C [auth D]1,603Homo sapiensMutation(s): 0 
Gene Names: DEPDC5KIAA0645
UniProt & NIH Common Fund Data Resources
Find proteins for O75140 (Homo sapiens)
Explore O75140 
Go to UniProtKB:  O75140
PHAROS:  O75140
GTEx:  ENSG00000100150 
Entity Groups  
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UniProt GroupO75140
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein AD [auth A]313Homo 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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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related GTP-binding protein CE [auth C]399Homo sapiensMutation(s): 1 
Gene Names: RRAGC
UniProt & NIH Common Fund Data Resources
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
F [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 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-15-1-0230
National Science Foundation (NSF, United States)United States2016197106
Howard Hughes Medical Institute (HHMI)United States--
Life Sciences Research FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Changes: Data collection, Database references
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.3: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-04-10
    Changes: Author supporting evidence, Data collection
  • Version 1.5: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.6: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.7: 2019-12-18
    Changes: Other
  • Version 1.8: 2024-03-13
    Changes: Data collection, Database references