8ZFZ

cryo-EM structure of Gs-coupled zebrafish GPR4 at pH 6.5

Summary for 8ZFZ

• Entry DOI: 10.2210/pdb8zfz/pdb
• Related: 8ZFJ
• EMDB information: 60072
• Descriptor: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1, scFv16, Guanine nucleotide-binding protein G(s) subunit alpha isoforms short, ... (5 entities in total)
• Functional Keywords: gpcr, membrane protein., signaling protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 5
• Total formula weight: 178904.22

Authors

Ma, Y.,Tang, M.,Ru, H.,Song, G. (deposition date: 2024-05-08, release date: 2025-01-22, Last modification date: 2025-07-23)

Primary citation

Ma, Y.,Wang, Y.,Tang, M.,Weng, Y.,Chen, Y.,Xu, Y.,An, S.,Wu, Y.,Zhao, S.,Xu, H.,Li, D.,Liu, M.,Lu, W.,Ru, H.,Song, G.
Cryo-EM structure of an activated GPR4-Gs signaling complex.
Nat Commun, 16:605-605, 2025

PubMed Abstract: G protein-coupled receptor 4 (GPR4) belongs to the subfamily of proton-sensing GPCRs (psGPCRs), which detect pH changes in extracellular environment and regulate diverse physiological responses. GPR4 was found to be overactivated in acidic tumor microenvironment as well as inflammation sites, with a triad of acidic residues within the transmembrane domain identified as crucial for proton sensing. However, the 3D structure remains unknown, and the roles of other conserved residues within psGPCRs are not well understood. Here we report cryo-electron microscopy (cryo-EM) structures of active zebrafish GPR4 at both pH 6.5 and 8.5, each highlighting a distribution of histidine and acidic residues at the extracellular region. Cell-based assays show that these ionizable residues moderately influence the proton-sensing capacity of zebrafish GPR4, compared to the more significant effects of the triad residues. Furthermore, we reveal a cluster of aromatic residues within the orthosteric pocket that may propagate the signaling to the intercellular region via repacking the aromatic patch at the central region. This study provides a framework for future signaling and functional investigation of psGPCRs.

PubMed: 39799123
DOI: 10.1038/s41467-025-55901-2

Experimental method

ELECTRON MICROSCOPY (3.3 Å)