The structure of human pregnane X receptor in complex with an SRC-1 coactivator peptide and a limonoid compound, nomilin

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Work: 0.194 

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Pregnane X receptor agonist nomilin extends lifespan and healthspan in preclinical models through detoxification functions.

Fan, S.Yan, Y.Xia, Y.Zhou, Z.Luo, L.Zhu, M.Han, Y.Yao, D.Zhang, L.Fang, M.Peng, L.Yu, J.Liu, Y.Gao, X.Guan, H.Li, H.Wang, C.Wu, X.Zhu, H.Cao, Y.Huang, C.

(2023) Nat Commun 14: 3368-3368

  • DOI: https://doi.org/10.1038/s41467-023-39118-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Citrus fruit has long been considered a healthy food, but its role and detailed mechanism in lifespan extension are not clear. Here, by using the nematode C. elegans, we identified that nomilin, a bitter-taste limoloid that is enriched in citrus, significantly extended the animals' lifespan, healthspan, and toxin resistance. Further analyses indicate that this ageing inhibiting activity depended on the insulin-like pathway DAF-2/DAF-16 and nuclear hormone receptors NHR-8/DAF-12. Moreover, the human pregnane X receptor (hPXR) was identified as the mammalian counterpart of NHR-8/DAF-12 and X-ray crystallography showed that nomilin directly binds with hPXR. The hPXR mutations that prevented nomilin binding blocked the activity of nomilin both in mammalian cells and in C. elegans. Finally, dietary nomilin supplementation improved healthspan and lifespan in D-galactose- and doxorubicin-induced senescent mice as well as in male senescence accelerated mice prone 8 (SAMP8) mice, and induced a longevity gene signature similar to that of most longevity interventions in the liver of bile-duct-ligation male mice. Taken together, we identified that nomilin may extend lifespan and healthspan in animals via the activation of PXR mediated detoxification functions.

  • Organizational Affiliation

    School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1
A, B
340Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
PHAROS:  Q15788
GTEx:  ENSG00000084676 
Find proteins for O75469 (Homo sapiens)
Explore O75469 
Go to UniProtKB:  O75469
PHAROS:  O75469
GTEx:  ENSG00000144852 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ15788O75469
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.986α = 90
b = 90.163β = 90
c = 106.391γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31670849
Ministry of Science and Technology (MoST, China)China2018YFC1004704

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description