9jfu

Cryo-EM structure of inactive GPR4 with NE52-QQ57

Structural highlights

9jfu is a 4 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.23Å
Ligands:	A1L1E
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

C562_ECOLX Electron-transport protein of unknown function.GPR4_HUMAN Proton-sensing G-protein coupled receptor couples to multiple intracellular signaling pathways, including GNAS/cAMP, GNAQ/phospholipase C (PLC), and GNA12/GNA13/Rho pathways (PubMed:12955148, PubMed:17462861, PubMed:20211729, PubMed:22110680). Acidosis-induced GPR4 activation increases paracellular gap formation and permeability of vascular endothelial cells through the GNA12/GNA13/Rho GTPase signaling pathway (PubMed:32058960). In the brain may mediate central respiratory sensitivity to CO(2)H(+) (By similarity).[UniProtKB:Q8BUD0]^[1] ^[2] ^[3] ^[4] ^[5]

Publication Abstract from PubMed

The regulation of pH homeostasis is crucial in many biological processes vital for survival, growth, and function of life. The pH-sensing G protein-coupled receptors (GPCRs), including GPR4, GPR65 and GPR68, play a pivotal role in detecting changes in extracellular proton concentrations, impacting both physiological and pathological states. However, comprehensive understanding of the proton sensing mechanism is still elusive. Here, we determined the cryo-electron microscopy structures of GPR4 and GPR65 in various activation states across different pH levels, coupled with G(s), G(q) or G(13) proteins, as well as a small molecule NE52-QQ57-bound inactive GPR4 structure. These structures reveal the dynamic nature of the extracellular loop 2 and its signature conformations in different receptor states, and disclose the proton sensing mechanism mediated by networks of extracellular histidine and carboxylic acid residues. Notably, we unexpectedly captured partially active intermediate states of both GPR4-G(s) and GPR4-G(q) complexes, and identified a unique allosteric binding site for NE52-QQ57 in GPR4. By integrating prior investigations with our structural analysis and mutagenesis data, we propose a detailed atomic model for stepwise proton sensation and GPCR activation. These insights may pave the way for the development of selective ligands and targeted therapeutic interventions for pH sensing-relevant diseases.

Structural basis of stepwise proton sensing-mediated GPCR activation.,Yue X, Peng L, Liu S, Zhang B, Zhang X, Chang H, Pei Y, Li X, Liu J, Shui W, Wu L, Xu H, Liu ZJ, Hua T Cell Res. 2025 Apr 11. doi: 10.1038/s41422-025-01092-w. PMID:40211064^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ludwig MG, Vanek M, Guerini D, Gasser JA, Jones CE, Junker U, Hofstetter H, Wolf RM, Seuwen K. Proton-sensing G-protein-coupled receptors. Nature. 2003 Sep 4;425(6953):93-8. PMID:12955148 doi:10.1038/nature01905
↑ Tobo M, Tomura H, Mogi C, Wang JQ, Liu JP, Komachi M, Damirin A, Kimura T, Murata N, Kurose H, Sato K, Okajima F. Previously postulated "ligand-independent" signaling of GPR4 is mediated through proton-sensing mechanisms. Cell Signal. 2007 Aug;19(8):1745-53. PMID:17462861 doi:10.1016/j.cellsig.2007.03.009
↑ Liu JP, Nakakura T, Tomura H, Tobo M, Mogi C, Wang JQ, He XD, Takano M, Damirin A, Komachi M, Sato K, Okajima F. Each one of certain histidine residues in G-protein-coupled receptor GPR4 is critical for extracellular proton-induced stimulation of multiple G-protein-signaling pathways. Pharmacol Res. 2010 Jun;61(6):499-505. PMID:20211729 doi:10.1016/j.phrs.2010.02.013
↑ Chen A, Dong L, Leffler NR, Asch AS, Witte ON, Yang LV. Activation of GPR4 by acidosis increases endothelial cell adhesion through the cAMP/Epac pathway. PLoS One. 2011;6(11):e27586. PMID:22110680 doi:10.1371/journal.pone.0027586
↑ Krewson EA, Sanderlin EJ, Marie MA, Akhtar SN, Velcicky J, Loetscher P, Yang LV. The Proton-Sensing GPR4 Receptor Regulates Paracellular Gap Formation and Permeability of Vascular Endothelial Cells. iScience. 2020 Feb 21;23(2):100848. PMID:32058960 doi:10.1016/j.isci.2020.100848
↑ Yue X, Peng L, Liu S, Zhang B, Zhang X, Chang H, Pei Y, Li X, Liu J, Shui W, Wu L, Xu H, Liu ZJ, Hua T. Structural basis of stepwise proton sensing-mediated GPCR activation. Cell Res. 2025 Apr 11. PMID:40211064 doi:10.1038/s41422-025-01092-w

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Ludwig MG, Vanek M, Guerini D, Gasser JA, Jones CE, Junker U, Hofstetter H, Wolf RM, Seuwen K. Proton-sensing G-protein-coupled receptors. Nature. 2003 Sep 4;425(6953):93-8. PMID:12955148 doi:10.1038/nature01905

[2] Tobo M, Tomura H, Mogi C, Wang JQ, Liu JP, Komachi M, Damirin A, Kimura T, Murata N, Kurose H, Sato K, Okajima F. Previously postulated "ligand-independent" signaling of GPR4 is mediated through proton-sensing mechanisms. Cell Signal. 2007 Aug;19(8):1745-53. PMID:17462861 doi:10.1016/j.cellsig.2007.03.009

[3] Liu JP, Nakakura T, Tomura H, Tobo M, Mogi C, Wang JQ, He XD, Takano M, Damirin A, Komachi M, Sato K, Okajima F. Each one of certain histidine residues in G-protein-coupled receptor GPR4 is critical for extracellular proton-induced stimulation of multiple G-protein-signaling pathways. Pharmacol Res. 2010 Jun;61(6):499-505. PMID:20211729 doi:10.1016/j.phrs.2010.02.013

[4] Chen A, Dong L, Leffler NR, Asch AS, Witte ON, Yang LV. Activation of GPR4 by acidosis increases endothelial cell adhesion through the cAMP/Epac pathway. PLoS One. 2011;6(11):e27586. PMID:22110680 doi:10.1371/journal.pone.0027586

[5] Krewson EA, Sanderlin EJ, Marie MA, Akhtar SN, Velcicky J, Loetscher P, Yang LV. The Proton-Sensing GPR4 Receptor Regulates Paracellular Gap Formation and Permeability of Vascular Endothelial Cells. iScience. 2020 Feb 21;23(2):100848. PMID:32058960 doi:10.1016/j.isci.2020.100848

[6] Yue X, Peng L, Liu S, Zhang B, Zhang X, Chang H, Pei Y, Li X, Liu J, Shui W, Wu L, Xu H, Liu ZJ, Hua T. Structural basis of stepwise proton sensing-mediated GPCR activation. Cell Res. 2025 Apr 11. PMID:40211064 doi:10.1038/s41422-025-01092-w

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9jfu

Cryo-EM structure of inactive GPR4 with NE52-QQ57

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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