9LWF | pdb_00009lwf

Cryo-EM structure of dual sensor bound GATOR2 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Cryo-EM structures of amino acid sensors bound to the human GATOR2 complex.

Su, M.Y.Teng, F.Wang, S.Mai, X.Zeng, H.Li, J.Song, X.Wang, X.Stjepanovic, G.

(2025) Cell Rep 44: 116088-116088

  • DOI: https://doi.org/10.1016/j.celrep.2025.116088
  • Primary Citation of Related Structures:  
    9LVJ, 9LVK, 9LWF

  • PubMed Abstract: 

    Mammalian cells regulate growth by integrating environmental cues through the mammalian target of rapamycin complex 1 (mTORC1) signaling pathway. The human GATOR2 complex, comprising WDR59, WDR24, Mios, Sec13, and Seh1l, is key to mTORC1 regulation. Under amino acid deprivation, GATOR2 is inhibited through interactions with cytosolic leucine sensor Sestrin2 and arginine sensor cytosolic arginine sensor for mTORC1 subunit 1 (CASTOR1). Amino acid abundance relieves this inhibition, allowing GATOR2 to antagonize the repressor GATOR1. Despite its importance, GATOR2's inhibition mechanisms were unclear. Here, we present cryo-electron microscopy (cryo-EM) structures of GATOR2 in three inhibitory states: CASTOR1 bound, Sestrin2 bound, and dual bound. CASTOR1 engages the Mios WD40 β-propellers, while Sestrin2 interacts with the WDR24-Seh1l subcomplex, inducing conformational movements. Hydrogen-deuterium exchange mass spectrometry (HDX-MS) reveals dynamic motions in apo-GATOR2 and its complexes with amino acid sensors, as well as the effects of amino acid supplementation. These findings unravel the interactions between GATOR2 and amino acid sensors, providing a perspective on the regulation of the mTORC1 pathway by nutrient-sensing machinery.


  • Organizational Affiliation
    • Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, SUSTech Homeostatic Medicine Institute, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China. Electronic address: sumy@sustech.edu.cn.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GATOR2 complex protein MIOSA,
B,
J [auth K],
K [auth L]
875Homo sapiensMutation(s): 0 
Gene Names: MIOS
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Go to UniProtKB:  Q9NXC5
PHAROS:  Q9NXC5
GTEx:  ENSG00000164654 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NXC5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GATOR2 complex protein WDR24
C, I
790Homo sapiensMutation(s): 0 
Gene Names: WDR24C16orf21JFP7
EC: 2.3.2.27
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PHAROS:  Q96S15
GTEx:  ENSG00000127580 
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UniProt GroupQ96S15
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GATOR2 complex protein WDR59D,
L [auth N]
974Homo sapiensMutation(s): 0 
Gene Names: WDR59KIAA1923FP977
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GTEx:  ENSG00000103091 
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UniProt GroupQ6PJI9
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform B of Nucleoporin SEH1421Homo sapiensMutation(s): 0 
Gene Names: SEH1LSEC13LSEH1
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Find proteins for Q96EE3 (Homo sapiens)
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GTEx:  ENSG00000085415 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 3 of Protein SEC13 homologH,
P [auth R]
368Homo sapiensMutation(s): 0 
Gene Names: SEC13D3S1231ESEC13ASEC13L1SEC13R
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Find proteins for P55735 (Homo sapiens)
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GTEx:  ENSG00000157020 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytosolic arginine sensor for mTORC1 subunit 1Q [auth U],
R [auth V]
329Homo sapiensMutation(s): 1 
Gene Names: CASTOR1GATSL3
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Find proteins for Q8WTX7 (Homo sapiens)
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PHAROS:  Q8WTX7
GTEx:  ENSG00000239282 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Sestrin-2S [auth X],
T [auth Y]
480Homo sapiensMutation(s): 1 
Gene Names: SESN2Hi95SEST2
EC: 1.11.1
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Find proteins for P58004 (Homo sapiens)
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PHAROS:  P58004
GTEx:  ENSG00000130766 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth B],
BA [auth B],
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth D],
HA [auth D],
IA [auth D],
JA [auth D],
KA [auth I],
LA [auth I],
MA [auth I],
NA [auth I],
OA [auth K],
PA [auth K],
QA [auth K],
RA [auth K],
SA [auth L],
TA [auth L],
U [auth A],
UA [auth L],
V [auth A],
VA [auth L],
W [auth A],
WA [auth N],
X [auth A],
XA [auth N],
Y [auth B],
YA [auth N],
Z [auth B],
ZA [auth N]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2025-08-13 
  • Deposition Author(s): Su, M.-Y.

Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release