Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Evolutionary study and structural basis of proton sensing by Mus GPR4 and Xenopus GPR4.
Journal, issue, pages	Cell, Vol. 188, Issue 3, Page 653-670.e24, Year 2025
Publish date	Feb 6, 2025
Authors	Xin Wen / Pan Shang / Haidi Chen / Lulu Guo / Naikang Rong / Xiaoyu Jiang / Xuan Li / Junyan Liu / Gongming Yang / Jiacheng Zhang / Kongkai Zhu / Qingbiao Meng / Xuefei He / Zhihai Wang / Zili Liu / Haoran Cheng / Yilin Zheng / Bifei Zhang / Jiaojiao Pang / Zhaoqian Liu / Peng Xiao / Yuguo Chen / Lunxu Liu / Fengming Luo / Xiao Yu / Fan Yi / Pengju Zhang / Fan Yang / Cheng Deng / Jin-Peng Sun /
PubMed Abstract	Animals have evolved pH-sensing membrane receptors, such as G-protein-coupled receptor 4 (GPR4), to monitor pH changes related to their physiology and generate adaptive reactions. However, the ...Animals have evolved pH-sensing membrane receptors, such as G-protein-coupled receptor 4 (GPR4), to monitor pH changes related to their physiology and generate adaptive reactions. However, the evolutionary trajectory and structural mechanism of proton sensing by GPR4 remain unresolved. Here, we observed a positive correlation between the optimal pH of GPR4 activity and the blood pH range across different species. By solving 7-cryoelectron microscopy (cryo-EM) structures of Xenopus tropicalis GPR4 (xtGPR4) and Mus musculus GPR4 (mmGPR4) under varying pH conditions, we identified that protonation of H and H enabled polar network establishment and tighter association between the extracellular loop 2 (ECL2) and 7 transmembrane (7TM) domain, as well as a conserved propagating path, which are common mechanisms underlying protonation-induced GPR4 activation across different species. Moreover, protonation of distinct extracellular H contributed to the more acidic optimal pH range of xtGPR4. Overall, our study revealed common and distinct mechanisms of proton sensing by GPR4, from a structural, functional, and evolutionary perspective.
External links	Cell / PubMed:39753131
Methods	EM (single particle)
Resolution	2.36 - 3.78 Å
Structure data	39946 8zd1 8zf4 EMDB-39946, PDB-8zd1: Cryo-EM structure of the xGPR4-Gs complex in pH6.2 PDB-8zf4: Cryo-EM structure of the receptor of xGPR4-Gs complex in pH6.2 Method: EM (single particle) / Resolution: 2.6 Å 60050 8zd1 8zf4 EMDB-60050, PDB-8zf4: Cryo-EM structure of the receptor of xGPR4-Gs complex in pH6.2 PDB-8zd1: Cryo-EM structure of the xGPR4-Gs complex in pH6.2 Method: EM (single particle) / Resolution: 3.05 Å 60051 8zf6 8zf7 EMDB-60051, PDB-8zf6: Cryo-EM structure of the xGPR4-Gs complex in pH6.7 PDB-8zf7: Cryo-EM structure of the receptor of xGPR4-Gs complex in pH6.7 Method: EM (single particle) / Resolution: 2.98 Å 60052 8zf7 EMDB-60052, PDB-8zf7: Cryo-EM structure of the receptor of xGPR4-Gs complex in pH6.7 Method: EM (single particle) / Resolution: 3.15 Å 60053 8zf9 8zfe EMDB-60053, PDB-8zf9: Cryo-EM structure of the mmGPR4-Gs complex in pH7.2 PDB-8zfe: Cryo-EM structure of the mmGPR4-Gs receptor in pH7.2 Method: EM (single particle) / Resolution: 2.56 Å 60054 8zfa 8zfb EMDB-60054, PDB-8zfa: Cryo-EM structure of the xtGPR4-Gs complex in pH7.2 PDB-8zfb: Cryo-EM structure of the receptor of xtGPR4-Gs complex in pH7.2 Method: EM (single particle) / Resolution: 2.96 Å 60055 8zfa 8zfb EMDB-60055, PDB-8zfb: Cryo-EM structure of the receptor of xtGPR4-Gs complex in pH7.2 PDB-8zfa: Cryo-EM structure of the xtGPR4-Gs complex in pH7.2 Method: EM (single particle) / Resolution: 3.78 Å 60056 8zfc 8zfd EMDB-60056, PDB-8zfc: Cryo-EM structure of the mmGPR4-Gs complex in pH7.6 PDB-8zfd: Cryo-EM structure of the mmGPR4-Gs receptor in pH7.6 Method: EM (single particle) / Resolution: 2.68 Å 60057 8zfc 8zfd EMDB-60057, PDB-8zfd: Cryo-EM structure of the mmGPR4-Gs receptor in pH7.6 PDB-8zfc: Cryo-EM structure of the mmGPR4-Gs complex in pH7.6 Method: EM (single particle) / Resolution: 2.56 Å 60058 8zf9 8zfe EMDB-60058, PDB-8zfe: Cryo-EM structure of the mmGPR4-Gs receptor in pH7.2 PDB-8zf9: Cryo-EM structure of the mmGPR4-Gs complex in pH7.2 Method: EM (single particle) / Resolution: 2.56 Å 61838 9jvg 9jvh EMDB-61838, PDB-9jvg: Cryo-EM structure of the mmGPR4-Gs complex in pH6.2 PDB-9jvh: Cryo-EM structure of the mmGPR4-Gs receptor in pH6.2 Method: EM (single particle) / Resolution: 2.76 Å 61839 9jvg 9jvh EMDB-61839, PDB-9jvh: Cryo-EM structure of the mmGPR4-Gs receptor in pH6.2 PDB-9jvg: Cryo-EM structure of the mmGPR4-Gs complex in pH6.2 Method: EM (single particle) / Resolution: 2.76 Å 61840 9jvm EMDB-61840, PDB-9jvm: Cryo-EM structure of the receptor of xGPR4-apo in pH8.0 Method: EM (single particle) / Resolution: 2.36 Å
Source	homo sapiens (human) xenopus tropicalis (tropical clawed frog) synthetic construct (others) mus musculus (house mouse)
Keywords	MEMBRANE PROTEIN/IMMUNE SYSTEM / pH6.2 / xGPR4 / Gs / MEMBRANE PROTEIN / MEMBRANE PROTEIN-IMMUNE SYSTEM complex / receptor / pH6.7 / pH7.2 / mmGPR4 / xtGPR4 / pH7.6 / pH8.0