9BOZ

Cryo-EM structure of human Glycine Receptor alpha3-beta heteromer in presence of glycine

Summary for 9BOZ

• Entry DOI: 10.2210/pdb9boz/pdb
• EMDB information: 44755
• Descriptor: Glycine receptor subunit alpha-3, Glycine receptor subunit beta,Green fluorescent protein, 2-acetamido-2-deoxy-beta-D-glucopyranose (3 entities in total)
• Functional Keywords: glycine receptor subunit alpha-3, glycine receptor subunit beta, green fluorescent protein, membrane protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 5
• Total formula weight: 273436.65

Authors

Liu, X.,Wang, W. (deposition date: 2024-05-06, release date: 2025-05-14, Last modification date: 2025-06-25)

Primary citation

Liu, X.,Krezel, M.,Wang, W.
Mechanism of human alpha 3 beta GlyR regulation by intracellular M3/M4 loop phosphorylation and 2,6-di-tert-butylphenol interaction.
Nat Commun, 16:5242-5242, 2025

PubMed Abstract: α3β glycine receptor (GlyR) is a subtype of GlyRs that belongs to the Cys-loop receptor superfamily. It is highly expressed in the spinal dorsal horn where sensory information is integrated. Under inflammatory conditions, the large unstructured intracellular M3/M4 loops of the α3 subunit are phosphorylated through the prostaglandin E2 (PGE) pathway, inhibiting ion conduction, and resulting in elevated pain sensation. A small molecule analgesic analog, 2,6-di-tert-butylphenol (2,6-DTBP) potentiates phosphorylated α3β GlyR through unclear mechanisms and relieves pain. Combining cryo-Electron Microscopy (cryo-EM) structures and single molecule Förster resonance energy transfer (smFRET) experiments, we show compaction of M3/M4 loop towards the ion conduction pore upon phosphorylation and further by 2,6-DTBP binding, which in turn modulates function through changing pore conformations and local electrostatics. We show that simultaneous interactions with the M3/M4 loop and the transmembrane domain (TM) is necessary for the potentiation of heteromeric α3β GlyR by 2,6-DTBP, while TM interaction alone is sufficient to potentiate homomeric α3 GlyR, explaining the mystery of why 2,6-DTBP potentiates only phosphorylated α3β GlyR. These findings show how post-translational modification of the unstructured intracellular M3/M4 loop may regulate Cys-loop receptor function, providing new perspectives in pain control and other pharmaceutical development targeting GlyRs and other Cys-loop receptors.

PubMed: 40473619
DOI: 10.1038/s41467-025-60516-8

Experimental method

ELECTRON MICROSCOPY (3.84 Å)