9JH6 | pdb_00009jh6

Activation mechanism of CYSLTR2 by C20:0


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 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

Sensing ceramides by CYSLTR2 and P2RY6 to aggravate atherosclerosis.

Zhang, S.Lin, H.Wang, J.Rui, J.Wang, T.Cai, Z.Huang, S.Gao, Y.Ma, T.Fan, R.Dai, R.Li, Z.Jia, Y.Chen, Q.He, H.Tan, J.Zhu, S.Gu, R.Dong, Z.Li, M.Xie, E.Fu, Y.Zheng, J.Jiang, C.Sun, J.Kong, W.

(2025) Nature 641: 476-485

  • DOI: https://doi.org/10.1038/s41586-025-08792-8
  • Primary Citation of Related Structures:  
    9JH5, 9JH6

  • PubMed Abstract: 

    Recent evidence has shown that increased levels of circulating long-chain ceramides predict atherosclerotic cardiovascular disease independently of cholesterol 1,2 . Although targeting ceramide signalling may provide therapeutic benefits beyond the treatment of hypercholesterolaemia, the underlying mechanism by which circulating ceramides aggravate atherosclerotic cardiovascular disease remains elusive. Here we examine whether circulating long-chain ceramides activate membrane G-protein-coupled receptors to exacerbate atherosclerosis. We perform a systematic screen that combines G-protein-signalling quantification, bioinformatic analysis of G-protein-coupled receptor expression and functional examination of NLRP3 inflammasome activation. The results suggest that CYSLTR2 and P2RY6 are potential endogenous receptors of C16:0 ceramide-induced inflammasome activation in both endothelial cells and macrophages. Inhibition of CYSLTR2 and P2RY6 genetically or pharmacologically alleviates ceramide-induced atherosclerosis aggravation. Moreover, increased ceramide levels correlate with the severity of coronary artery disease in patients with varying degrees of renal impairment. Notably, CYSLTR2 and P2RY6 deficiency mitigates chronic-kidney-disease-aggravated atherosclerosis in mice without affecting cholesterol or ceramide levels. Structural analyses of ceramide-CYSLTR2-G q complexes reveal that both C16:0 and C20:0 ceramides bind in an inclined channel-like ligand-binding pocket on CYSLTR2. We further reveal an unconventional mechanism underlying ceramide-induced CYSLTR2 activation and the CYSLTR2-G q interface. Overall, our study provides structural and molecular mechanisms of how long-chain ceramides initiate transmembrane G q and inflammasome signalling through direct binding to CYSLTR2 and P2RY6 receptors. Therefore, blocking these signals may provide a new therapeutic potential to treat atherosclerosis-related diseases.


  • Organizational Affiliation
    • Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, P. R. China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cysteinyl leukotriene receptor 2A [auth R]346Homo sapiensMutation(s): 1 
Gene Names: CYSLTR2CYSLT2CYSLT2R
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NS75 (Homo sapiens)
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Go to UniProtKB:  Q9NS75
PHAROS:  Q9NS75
GTEx:  ENSG00000152207 
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UniProt GroupQ9NS75
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2B [auth C]59Homo sapiensMutation(s): 0 
Gene Names: GNG2
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Find proteins for P59768 (Homo sapiens)
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16C [auth S]250Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1D [auth A]361Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1E [auth B]358Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Nb35F [auth N]151Lama glamaMutation(s): 0 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1LXR
Query on A1LXR

Download Ideal Coordinates CCD File 
G [auth R]Cer(d18:0/20:0)
C38 H77 N O3
ZWAUSWHRQBSECP-PQQNNWGCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32130055
National Natural Science Foundation of China (NSFC)China92057121

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Data collection, Database references