9OTI | pdb_00009oti

GATOR2 complex bound to arginine sensor CASTOR1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for mTORC1 regulation by the CASTOR1-GATOR2 complex.

Jansen, R.M.Maghe, C.Tapia, K.Wu, S.Yang, S.Ren, X.Zoncu, R.Hurley, J.H.

(2025) Nat Struct Mol Biol 32: 1980-1988

  • DOI: https://doi.org/10.1038/s41594-025-01635-0
  • Primary Citation of Related Structures:  
    9OTI

  • PubMed Abstract: 

    Mechanistic target of rapamycin complex 1 (mTORC1) is a nutrient-responsive master regulator of metabolism. Amino acids control the recruitment and activation of mTORC1 at the lysosome through the nucleotide loading state of the heterodimeric Rag GTPases. Under low nutrients, including arginine, the GTPase-activating protein complex GATOR1 promotes GTP hydrolysis on RagA/B, inactivating mTORC1. GATOR1 is regulated by the cage-like GATOR2 complex and cytosolic amino acid sensors. To understand how the arginine sensor CASTOR1 binds to GATOR2 to disinhibit GATOR1 under low cytosolic arginine, we determined the cryo-electron microscopy structure of human GATOR2 bound to CASTOR1 in the absence of arginine. Two MIOS WD40 domain β-propellers of the GATOR2 cage engage with both subunits of a single CASTOR1 homodimer. Each propeller binds to a negatively charged MIOS-binding interface on CASTOR1 that is distal to the arginine pocket. The structure shows how arginine-triggered loop ordering in CASTOR1 blocks the MIOS-binding interface, switches off its binding to GATOR2 and, thus, communicates to downstream mTORC1 activation.


  • Organizational Affiliation
    • Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GATOR2 complex protein MIOSA,
B,
I [auth L],
P [auth T]
875Homo sapiensMutation(s): 0 
Gene Names: MIOS
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXC5 (Homo sapiens)
Explore Q9NXC5 
Go to UniProtKB:  Q9NXC5
PHAROS:  Q9NXC5
GTEx:  ENSG00000164654 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NXC5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GATOR complex protein WDR24C,
J [auth M]
790Homo sapiensMutation(s): 0 
Gene Names: WDR24C16orf21JFP7
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96S15 (Homo sapiens)
Explore Q96S15 
Go to UniProtKB:  Q96S15
PHAROS:  Q96S15
GTEx:  ENSG00000127580 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96S15
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
GATOR complex protein WDR59D,
K [auth N]
974Homo sapiensMutation(s): 0 
Gene Names: WDR59KIAA1923FP977
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PJI9 (Homo sapiens)
Explore Q6PJI9 
Go to UniProtKB:  Q6PJI9
PHAROS:  Q6PJI9
GTEx:  ENSG00000103091 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6PJI9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoporin SEH1360Homo sapiensMutation(s): 0 
Gene Names: SEH1LSEC13LSEH1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EE3 (Homo sapiens)
Explore Q96EE3 
Go to UniProtKB:  Q96EE3
PHAROS:  Q96EE3
GTEx:  ENSG00000085415 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EE3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SEC13 homologH,
O [auth R]
322Homo sapiensMutation(s): 0 
Gene Names: SEC13D3S1231ESEC13ASEC13L1SEC13R
UniProt & NIH Common Fund Data Resources
Find proteins for P55735 (Homo sapiens)
Explore P55735 
Go to UniProtKB:  P55735
PHAROS:  P55735
GTEx:  ENSG00000157020 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55735
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytosolic arginine sensor for mTORC1 subunit 1Q [auth U],
R [auth V]
329Homo sapiensMutation(s): 2 
Gene Names: CASTOR1GATSL3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTX7 (Homo sapiens)
Explore Q8WTX7 
Go to UniProtKB:  Q8WTX7
PHAROS:  Q8WTX7
GTEx:  ENSG00000239282 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WTX7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv3.3.1

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 StatesCA285366

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-01
    Type: Initial release
  • Version 1.1: 2025-10-29
    Changes: Data collection, Database references