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Structure paper

TitleStructural basis for cholesterol sensing of LYCHOS and its interaction with indoxyl sulfate.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 2815, Year 2025
Publish dateMar 21, 2025
AuthorsZhenhua Wang / Jingjing He / Yufan Yang / Yonglin He / Hongwu Qian /
PubMed AbstractThe 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 ...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.
External linksNat Commun / PubMed:40118871 / PubMed Central
MethodsEM (single particle)
Resolution3.1 - 3.5 Å
Structure data

37761

8wr3

EMDB-37761, PDB-8wr3:
Cryo-EM structure of lysosomal protein LYCHOS
Method: EM (single particle) / Resolution: 3.1 Å

61127

9j3x

EMDB-61127, PDB-9j3x:
Cryo-EM structure of lysosome cholesterol sencing protein LYCHOS in Tight-state
Method: EM (single particle) / Resolution: 3.3 Å

61128

9j3z

EMDB-61128, PDB-9j3z:
Cryo-EM structure of lysosome cholesterol sencing protein in L state
Method: EM (single particle) / Resolution: 3.5 Å

61129

9j40

EMDB-61129, PDB-9j40:
Cryo-EM structure of lysosome cholesterol sencing protein complex
Method: EM (single particle) / Resolution: 3.4 Å

Chemicals

ChemComp-CLR:
CHOLESTEROL

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-IOS:
3-SULFOOXY-1H-INDOLE / toxin*YM

ChemComp-TRP:
TRYPTOPHAN

Source
  • homo sapiens (human)
  • nomascus leucogenys (northern white-cheeked gibbon)
KeywordsTRANSPORT PROTEIN / lysosome / tranporter / amino acids / LIPID BINDING PROTEIN

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