9JCP

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

This is a non-PDB format compatible entry.

Summary for 9JCP

• Entry DOI: 10.2210/pdb9jcp/pdb
• EMDB information: 61371
• Descriptor: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2, Nanobody 35, ... (8 entities in total)
• Functional Keywords: cryo-em, gpcr, proton-sensing, gpr4, ph 7.4, gq, complex, signaling protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 5
• Total formula weight: 161868.92

Authors

Xu, H.E.,You, C.,Jiang, Y. (deposition date: 2024-08-30, release date: 2025-07-09)

Primary citation

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.
Molecular mechanism of pH sensing and activation in GPR4 reveals proton-mediated GPCR signaling.
Cell Discov, 11:59-59, 2025

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.

PubMed: 40555728
DOI: 10.1038/s41421-025-00807-y

Experimental method

ELECTRON MICROSCOPY (2.55 Å)