8Y56 | pdb_00008y56

Cryo-EM reveals cholesterol binding in the lysosomal GPCR-like protein LYCHOS


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM reveals cholesterol binding in the lysosomal GPCR-like protein LYCHOS.

Zhao, J.Shen, Q.Yong, X.Li, X.Tian, X.Sun, S.Xu, Z.Zhang, X.Zhang, L.Yang, H.Shao, Z.Xu, H.Jiang, Y.Zhang, Y.Yan, W.

(2025) Nat Struct Mol Biol 32: 896-904

  • DOI: https://doi.org/10.1038/s41594-024-01470-9
  • Primary Citation of Related Structures:  
    8Y56

  • PubMed Abstract: 

    Cholesterol plays a pivotal role in modulating the activity of mechanistic target of rapamycin complex 1 (mTOR1), thereby regulating cell growth and metabolic homeostasis. LYCHOS, a lysosome-localized G-protein-coupled receptor-like protein, emerges as a cholesterol sensor and is capable of transducing the cholesterol signal to affect the mTORC1 function. However, the precise mechanism by which LYCHOS recognizes cholesterol remains unknown. Here, using cryo-electron microscopy, we determined the three-dimensional structural architecture of LYCHOS in complex with cholesterol molecules, revealing a unique arrangement of two sequential structural domains. Through a comprehensive analysis of this structure, we elucidated the specific structural features of these two domains and their collaborative role in the process of cholesterol recognition by LYCHOS.


  • Organizational Affiliation
    • Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysosomal cholesterol signaling proteinA [auth R]840Homo sapiensMutation(s): 0 
Gene Names: GPR155PGR22
Membrane Entity: Yes 
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DKB
Query on DKB

Download Ideal Coordinates CCD File 
H [auth R][(2R)-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] octadecanoate
C39 H78 N O8 P
RPJZYOHZALDGKI-DIPNUNPCSA-N
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
C [auth R],
D [auth R],
E [auth R],
F [auth R],
G [auth R]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
B [auth R]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 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
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release
  • Version 1.1: 2025-06-04
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-23
    Changes: Data collection