9LMO

Cryo-EM structure of human apo inactive GPR4

Summary for 9LMO

• Entry DOI: 10.2210/pdb9lmo/pdb
• EMDB information: 39864 63219
• Descriptor: Heavy chain of anti-Bril Fab, anti-Fab Nanobody, Light chain of anti-Bril Fab, ... (4 entities in total)
• Functional Keywords: gpcr, class a, gpr4, cryo-em, protein sensing, inactive state, membrane protein/immune system, membrane protein-immune system complex
• Biological source: Homo sapiens; More
• Total number of polymer chains: 4
• Total formula weight: 114766.63

Authors

Chen, L.N.,Zhou, H.,Xi, K.,Cheng, S.Z.,Liu, Y.F.,Fu, Y.F.,Ma, X.Y.,Xu, P.,Ji, S.Y.,Wang, W.W.,Shen, D.D.,Zhang, H.B.,Shen, Q.Y.,Chai, R.,Zhang, M.,Yang, L.,Han, F.,Mao, C.Y.,Cai, X.J.,Zhang, Y. (deposition date: 2025-01-19, release date: 2025-07-09, Last modification date: 2026-01-14)

Primary citation

Chen, L.N.,Zhou, H.,Xi, K.,Cheng, S.,Liu, Y.,Fu, Y.,Ma, X.,Xu, P.,Ji, S.Y.,Wang, W.W.,Shen, D.D.,Zhang, H.,Shen, Q.,Chai, R.,Zhang, M.,Yang, L.,Han, F.,Mao, C.,Cai, X.,Zhang, Y.
Proton perception and activation of a proton-sensing GPCR.
Mol.Cell, 85:1640-1657.e8, 2025

PubMed Abstract: Maintaining pH at cellular, tissular, and systemic levels is essential for human health. Proton-sensing GPCRs regulate physiological and pathological processes by sensing the extracellular acidity. However, the molecular mechanism of proton sensing and activation of these receptors remains elusive. Here, we present cryoelectron microscopy (cryo-EM) structures of human GPR4, a prototypical proton-sensing GPCR, in its inactive and active states. Our studies reveal that three extracellular histidine residues are crucial for proton sensing of human GPR4. The binding of protons induces substantial conformational changes in GPR4's ECLs, particularly in ECL2, which transforms from a helix-loop to a β-turn-β configuration. This transformation leads to the rearrangements of H-bond network and hydrophobic packing, relayed by non-canonical motifs to accommodate G proteins. Furthermore, the antagonist NE52-QQ57 hinders human GPR4 activation by preventing hydrophobic stacking rearrangement. Our findings provide a molecular framework for understanding the activation mechanism of a human proton-sensing GPCR, aiding future drug discovery.

PubMed: 40215960
DOI: 10.1016/j.molcel.2025.02.030

Experimental method

ELECTRON MICROSCOPY (3.2 Å)