8Y63 | pdb_00008y63

Cryo-EM structure of the C20:0 ceramide-bound FPR2-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Metabolic signaling of ceramides through the FPR2 receptor inhibits adipocyte thermogenesis.

Lin, H.Ma, C.Cai, K.Guo, L.Wang, X.Lv, L.Zhang, C.Lin, J.Zhang, D.Ye, C.Wang, T.Huang, S.Han, J.Zhang, Z.Gao, J.Zhang, M.Pu, Z.Li, F.Guo, Y.Zhou, X.Qin, C.Yi, F.Yu, X.Kong, W.Jiang, C.Sun, J.P.

(2025) Science 388: eado4188-eado4188

  • DOI: https://doi.org/10.1126/science.ado4188
  • Primary Citation of Related Structures:  
    8Y62, 8Y63, 9JHJ

  • PubMed Abstract: 

    Ceramides play a central role in human health and disease, yet their role as systemic signaling molecules remain poorly understood. In this work, we identify FPR2 as a membrane receptor that specifically binds long-chain ceramides (C14-C20). In brown and beige adipocytes, C16:0 ceramide binding to FPR2 inhibits thermogenesis via G i -cyclic AMP signaling pathways, an effect that is reversed in the absence of FPR2. We present three cryo-electron microscopy structures of FPR2 in complex with G i trimers bound to C16:0, C18:0 and C20:0 ceramides. The hydrophobic tails are deeply embedded in the orthosteric ligand pocket, which has a limited amount of plasticity. Modification of the ceramide binding motif in closely related receptors, such as FPR1 or FPR3, converts them from inactive to active ceramide receptors. Our findings provide a structural basis for adipocyte thermogenesis mediated by FPR2.


  • Organizational Affiliation
    • Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-formyl peptide receptor 2A [auth R]351Homo sapiensMutation(s): 0 
Gene Names: FPR2
UniProt & NIH Common Fund Data Resources
Find proteins for P25090 (Homo sapiens)
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PHAROS:  P25090
GTEx:  ENSG00000171049 
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UniProt GroupP25090
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1B [auth A]354Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
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Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [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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UniProt GroupP62873
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth C]58Homo sapiensMutation(s): 0 
Gene Names: GNG2
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PHAROS:  P59768
GTEx:  ENSG00000186469 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16285synthetic constructMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1LXR (Subject of Investigation/LOI)
Query on A1LXR

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2025-03-19
    Changes: Data collection, Database references
  • Version 1.3: 2025-03-26
    Changes: Data collection, Database references
  • Version 1.4: 2025-05-14
    Changes: Data collection, Database references
  • Version 1.5: 2025-06-18
    Changes: Data collection, Database references