9JCQ | pdb_00009jcq

Cryo-EM structure of the proton-sensing GPCR (GPR4)-Gs protein complex at pH 7.4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Molecular mechanism of pH sensing and activation in GPR4 reveals proton-mediated GPCR signaling.

You, C.Guo, S.Zhang, T.He, X.Gao, T.Xin, W.Zhu, Z.Lu, Y.Xu, Y.Li, Z.Zhang, Y.Cheng, X.Jiang, Y.Xie, X.Xu, H.E.

(2025) Cell Discov 11: 59-59

  • DOI: https://doi.org/10.1038/s41421-025-00807-y
  • Primary Citation of Related Structures:  
    9JCO, 9JCP, 9JCQ

  • PubMed Abstract: 

    Maintaining pH homeostasis is critical for cellular function across all living organisms. Proton-sensing G protein-coupled receptors (GPCRs), particularly GPR4, play a pivotal role in cellular responses to pH changes. Yet, the molecular mechanisms underlying their proton sensing and activation remain incompletely understood. Here we present high-resolution cryo-electron microscopy structures of GPR4 in complex with G proteins under physiological and acidic pH conditions. Our structures reveal an intricate proton-sensing mechanism driven by a sophisticated histidine network in the receptor's extracellular domain. Upon protonation of key histidines under acidic conditions, a remarkable conformational cascade is initiated, propagating from the extracellular region to the intracellular G protein-coupling interface. This dynamic process involves precise transmembrane helix rearrangements and conformational shifts of conserved motifs, mediated by strategically positioned water molecules. Notably, we discovered a bound bioactive lipid, lysophosphatidylcholine, which has positive allosteric effects on GPR4 activation. These findings provide a comprehensive framework for understanding proton sensing in GPCRs and the interplay between pH sensing and lipid regulation, offering insights into cellular pH homeostasis and potential therapies for pH-related disorders.


  • Organizational Affiliation

    The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. youchongzhao@gmail.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(s) subunit alpha361Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1518Homo 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: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]70Homo sapiensMutation(s): 0 
Gene Names: GNG2
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GTEx:  ENSG00000186469 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody 35D [auth N]128Lama glamaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
G-protein coupled receptor 4E [auth D]362Homo sapiensMutation(s): 0 
Gene Names: GPR4
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Find proteins for P46093 (Homo sapiens)
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GTEx:  ENSG00000177464 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 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)China--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release