9JBJ | pdb_00009jbj

Cryo-EM structure of the human LYCHOS Y57A/R61A mutant in the expanded state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 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 insights into cholesterol sensing by the LYCHOS-mTORC1 pathway.

Yu, S.Ding, J.H.Wang, J.L.Wang, W.Zuo, P.Yang, A.Dai, Z.Yin, Y.Sun, J.P.Liang, L.

(2025) Nat Commun 16: 6792-6792

  • DOI: https://doi.org/10.1038/s41467-025-61966-w
  • Primary Citation of Related Structures:  
    9JBE, 9JBF, 9JBG, 9JBH, 9JBI, 9JBJ

  • PubMed Abstract: 

    The lysosomal cholesterol sensor LYCHOS regulates mTORC1 signaling by coupling cholesterol sensing to GATOR1-Rag GTPase modulation, yet its structural mechanisms remain unclear. Here we report six cryo-electron microscopy structures of human LYCHOS, depicting five distinct states. These are categorized into a contracted state when complexed with a sufficient amount of the cholesterol analogue cholesteryl hemisuccinate (CHS), and an expanded state when CHS is deficient. The structure forms a homodimer, within each monomer the transmembrane region is divided into a permease-like domain (PLD) and a GPCR-like domain (GLD) with two clearly defined adjacent cholesterol binding sites between them. Cholesterol binding induces a translation of GLD towards PLD and exposes the cytosolic extension of transmembrane 15, which interacts with GATOR1. Our results elucidate the structural mechanism of cholesterol sensing by the mTORC1 pathway, providing a structural basis for developing inhibitors that selectively target mTORC1 pathway by blocking LYCHOS in its expanded state.


  • Organizational Affiliation
    • Department of Biophysics, State Key Laboratory of Natural and Biomimetic Drugs, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysosomal cholesterol signaling protein
A, B
878Homo sapiensMutation(s): 2 
Gene Names: GPR155PGR22
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z3F1 (Homo sapiens)
Explore Q7Z3F1 
Go to UniProtKB:  Q7Z3F1
PHAROS:  Q7Z3F1
GTEx:  ENSG00000163328 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z3F1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32171224

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Data collection, Database references