8WR3 | pdb_00008wr3

Cryo-EM structure of lysosomal protein LYCHOS


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for cholesterol sensing of LYCHOS and its interaction with indoxyl sulfate.

Wang, Z.He, J.Yang, Y.He, Y.Qian, H.

(2025) Nat Commun 16: 2815-2815

  • DOI: https://doi.org/10.1038/s41467-025-58087-9
  • Primary Citation of Related Structures:  
    8WR3, 9J3X, 9J3Z, 9J40

  • PubMed Abstract: 

    The lysosome serves as an essential nutrient-sensing hub within the cell, where the mechanistic target of rapamycin complex 1 (mTORC1) is activated. Lysosomal cholesterol signaling (LYCHOS), a lysosome membrane protein, has been identified as a cholesterol sensor that couples cholesterol concentration to mTORC1 activation. However, the molecular basis is unknown. Here, we determine the cryo-electron microscopy (cryo-EM) structure of human LYCHOS at a resolution of 3.1 Å, revealing a cholesterol-like density at the interface between the permease and G-protein coupled receptor (GPCR) domains. Advanced 3D classification reveals two distinct states of LYCHOS. Comparative structural analysis between these two states demonstrated a cholesterol-related movement of GPCR domain relative to permease domain, providing structural insights into how LYCHOS senses lysosomal cholesterol levels. Additionally, we identify indoxyl sulfate (IS) as a binding ligand to the permease domain, confirmed by the LYCHOS-IS complex structure. Overall, our study provides a foundation and indicates additional directions for further investigation of the essential role of LYCHOS in the mTORC1 signaling pathway.


  • Organizational Affiliation
    • Department of Cardiology, The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lysosomal cholesterol signaling protein
A, B
718Homo sapiensMutation(s): 1 
Gene Names: GPR155
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q7Z3F1-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV (Subject of Investigation/LOI)
Query on POV

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
G [auth A]
I [auth B]
J [auth B]
D [auth A],
E [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth B]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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
Other privateChinaKY9100000034

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-04-02
    Changes: Data collection, Database references
  • Version 1.2: 2025-04-09
    Changes: Data collection, Database references
  • Version 1.3: 2025-07-02
    Changes: Data collection