9DX0 | pdb_00009dx0

Human GATOR2 complex - apo state

• PDB DOI: https://doi.org/10.2210/pdb9DX0/pdb
• EM Map EMD-47276: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-10-10 Released: 2026-05-20 
• Deposition Author(s): Wranik, M., Rogala, K.B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), Department of Defense (DOD, United States), Lustgarten Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.47 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for the dynamic regulation of mTORC1 by amino acids.

Valenstein, M.L., Wranik, M., Lalgudi, P.V., Linde-Garelli, K.Y., Choi, Y., Chivukula, R.R., Sabatini, D.M., Rogala, K.B.

(2025) Nature 646: 493-500

• PubMed: 40836086 
• DOI: https://doi.org/10.1038/s41586-025-09428-7
• Primary Citation Related Structures: 
  9DX0, 9DX1, 9DX2


• PubMed Abstract: 
  

  The mechanistic target of rapamycin complex 1 (mTORC1) anchors a conserved signalling pathway that regulates growth in response to nutrient availability ^1-5 . Amino acids activate mTORC1 through the Rag GTPases, which are regulated by GATOR, a supercomplex consisting of GATOR1, KICSTOR and the nutrient-sensing hub GATOR2 (refs. ^6-9 ). GATOR2 forms an octagonal cage, with its distinct WD40 domain β-propellers interacting with GATOR1 and the leucine sensors Sestrin1 and Sestrin2 (SESN1 and SESN2) and the arginine sensor CASTOR1 (ref. ¹⁰ ). The mechanisms through which these sensors regulate GATOR2 and how they detach from it upon binding their cognate amino acids remain unknown. Here, using cryo-electron microscopy, we determined the structures of a stabilized GATOR2 bound to either Sestrin2 or CASTOR1. The sensors occupy distinct and non-overlapping binding sites, disruption of which selectively impairs the ability of mTORC1 to sense individual amino acids. We also resolved the apo (leucine-free) structure of Sestrin2 and characterized the amino acid-induced structural rearrangements within Sestrin2 and CASTOR1 that trigger their dissociation from GATOR2. Binding of either sensor restricts the dynamic WDR24 β-propeller of GATOR2, a domain essential for nutrient-dependent mTORC1 activation. These findings reveal the allosteric mechanisms that convey amino acid sufficiency to GATOR2 and the ensuing structural changes that lead to mTORC1 activation.

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Organizational Affiliation: 
• Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
Whitehead Institute for Biomedical Research, Cambridge, MA, USA.
Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
Harvard Medical School, Boston, MA, USA.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.
Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
Department of Surgery, Massachusetts General Hospital, Boston, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic. [e-mail].
Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Boston Branch, Cambridge, MA, USA. [e-mail].
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].
Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 424.54 kDa 
• Atom Count: 27,053 
• Modeled Residue Count: 3,727 
• Deposited Residue Count: 3,764 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GATOR2 complex protein MIOS	A, B	1,113	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GATOR2 complex protein WDR24	C	905	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein SEC13 homolog	D	633	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.47 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC	4.5

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-20 
Deposition Author(s): Wranik, M., Rogala, K.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM150935
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R00 CA255926
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30 CA124435
Department of Defense (DOD, United States)	United States	CA220856
Lustgarten Foundation	United States	1156790

Revision History  

• Version 1.0: 2026-05-20
  Type: Initial release