8Y56 | pdb_00008y56

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

• PDB DOI: https://doi.org/10.2210/pdb8Y56/pdb
• EM Map EMD-38930: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2024-01-31 Released: 2025-01-29 
• Deposition Author(s): Zhao, J., Shen, Q.Y., Zhang, Y., Shao, Z.H.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

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

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

• PubMed: 39824976 
• DOI: https://doi.org/10.1038/s41594-024-01470-9
• Primary Citation 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.

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Organizational Affiliation: 
• Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.
Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, China.
Department of Pathology of Sir Run Shaw Hospital, Department of Pharmacology, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China.
MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, China.
NHC Key Lab of Transplant Engineering and Immunology, Regenerative Medicine Research Center, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, Metabolomics and Proteomics Technology Platform, West China Hospital, Sichuan University, Chengdu, China.
Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China. [e-mail].
Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, China. [e-mail].
New Cornerstone Science Laboratory & Liangzhu Laboratory, the Second Affiliated Hospital & School of Basic Medical Sciences, Zhejiang University, Hangzhou, China. [e-mail].
Department of Hepatobiliary Surgery, Innovative Institute of Tumor Immunity and Medicine (ITIM), Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, The First Affiliated Hospital of Anhui Medical University, Hefei, China. [e-mail].
Department of Pathology of Sir Run Shaw Hospital, Department of Pharmacology, and Liangzhu Laboratory, Zhejiang University School of Medicine, Hangzhou, China. [e-mail].
MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, China. [e-mail].
Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 96.55 kDa 
• Atom Count: 4,796 
• Modeled Residue Count: 586 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysosomal cholesterol signaling protein	A [auth R]	840	Homo sapiens	Mutation(s): 0  Gene Names: GPR155, PGR22 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DKB	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)	C [auth R], D [auth R], E [auth R], F [auth R], G [auth R]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
NA	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:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Zhao, J., Shen, Q.Y., Zhang, Y., Shao, Z.H.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• 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