Article | Published:

Architecture of the human GATOR1 and GATOR1–Rag GTPases complexes

Nature volume 556, pages 6469 (05 April 2018) | Download Citation

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.

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Acknowledgements

We thank all members of the Sabatini laboratory and T. Schwartz for insights; P. Abeyrathne, N. Grigorieff, R. Grant and C. Drennan for technical support; R. Saxton, M. Pacold and S. Shan for critical reading of the manuscript. This work was supported by grants from the NIH (R01 CA103866, R01 CA129105 and R37 AI047389) and Department of Defense (W81XWH-15-1-0230) to D.M.S., fellowship support from NSF (2016197106) to K.J.C. and from the Life Sciences Research Foundation to K.S., where he is a Pfizer Fellow. R.K.H., C.H. and Z.Y. were supported by the Howard Hughes Medical Institute. D.M.S. is an investigator of the Howard Hughes Medical Institute.

Author information

Author notes

    • Lynne Chantranupong

    Present address: Harvard Medical School, 200 Longwood Avenue, Boston, Massachusetts 02115, USA.

    • Kuang Shen
    •  & Rick K. Huang

    These authors contributed equally to this work.

Affiliations

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

    • Kuang Shen
    • , Kendall J. Condon
    • , Max L. Valenstein
    • , Lynne Chantranupong
    • , Aimaiti Bomaliyamu
    • , Abigail Choe
    •  & David M. Sabatini
  2. Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA

    • Kuang Shen
    • , Edward J. Brignole
    • , Kendall J. Condon
    • , Max L. Valenstein
    • , Lynne Chantranupong
    •  & David M. Sabatini
  3. Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA

    • Kuang Shen
    • , Kendall J. Condon
    • , Max L. Valenstein
    • , Lynne Chantranupong
    •  & David M. Sabatini
  4. Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA

    • Kuang Shen
    • , Kendall J. Condon
    • , Max L. Valenstein
    • , Lynne Chantranupong
    •  & David M. Sabatini
  5. Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA

    • Rick K. Huang
    • , Chuan Hong
    •  & Zhiheng Yu
  6. Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA

    • Edward J. Brignole

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Contributions

K.S. and D.M.S. initiated the project. K.S. purified the proteins and performed the biochemical characterization with input from K.J.C., M.L.V., L.C., A.B., and A.C. R.K.H., C.H. and Z.Y. determined the electron microscopy density maps for GATOR1 and GATOR1–Rag GTPases. K.S. and E.J.B. built the structural model. K.S., R.K.H., E.J.B., Z.Y. and D.M.S. wrote and edited the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Zhiheng Yu or David M. Sabatini.

Reviewer Information Nature thanks D. Barford, K. Inoki and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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  2. 2.

    Supplementary Figure

    This file contains Supplementary Figure 1 which shows the uncropped gel pictures for all the western blot analyses in the article.

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    Supplementary Table

    This file contains Supplementary Table 1 which shows the EM data collection and model refinement.

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    This file contains Supplementary Material and Methods.

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DOI

https://doi.org/10.1038/nature26158

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