9JCQ | pdb_00009jcq

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

• PDB DOI: https://doi.org/10.2210/pdb9JCQ/pdb
• EM Map EMD-61372: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens, Lama glama
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2024-08-30 Released: 2025-07-09 
• Deposition Author(s): You, C., Xu, H.E., Jiang, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

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

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

• PubMed: 40555728 
• DOI: https://doi.org/10.1038/s41421-025-00807-y
• Primary Citation 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.

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Organizational Affiliation: 
• The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Lingang Laboratory, Shanghai, China.
University of Chinese Academy of Sciences, Beijing, China.
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China.
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China.
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Lingang Laboratory, Shanghai, China. [e-mail].
The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang, China. [e-mail].
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China. [e-mail].
Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong, China. [e-mail].
The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
School of Life Science and Technology, ShanghaiTech University, Shanghai, China. [e-mail].
Lingang Laboratory, Shanghai, China. [e-mail].
School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 162.41 kDa 
• Atom Count: 8,431 
• Modeled Residue Count: 1,051 
• Deposited Residue Count: 1,439 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(s) subunit alpha	A	361	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	518	Homo sapiens	Mutation(s): 0  Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873  Go to UniProtKB:  P62873
PHAROS:  P62873 GTEx:  ENSG00000078369

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C [auth G]	70	Homo sapiens	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768  Go to UniProtKB:  P59768
PHAROS:  P59768 GTEx:  ENSG00000186469

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody 35	D [auth N]	128	Lama glama	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled receptor 4	E [auth D]	362	Homo sapiens	Mutation(s): 0  Gene Names: GPR4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P46093 (Homo sapiens) Explore P46093  Go to UniProtKB:  P46093
PHAROS:  P46093 GTEx:  ENSG00000177464

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CLR	H [auth D], I [auth D]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
A1L35 (Subject of Investigation/LOI)	F [auth D], G [auth D]	2-[[(2~{R})-3-acetyloxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium C10 H23 N O7 P RYCNUMLMNKHWPZ-SNVBAGLBSA-O

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): You, C., Xu, H.E., Jiang, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

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