Predicted conformations of 5-HT3 receptor ion channels are modified by subunit D

Serotonin type 3 (5-HT₃) receptors are ligand gated ion channels having five separate subunits (A, B, C, D, and E) that participate in formation of functional homomers (5HT3A subunit only) or heteromers with 5HT3A subunits. Since there is limited information available about the participation of the 5HT3D subunit in heteromer formation and channel pore interfaces, we explored how the 5HT3D subunit and its SNP mutated proteins contribute to conformational transitions. We generated homology models of the full-length human 5HT3D, and non-synonymous SNPs, subunits based on crystal and cryo-EM mouse 5HT3A subunit structures enabling development of heteromeric receptor models in A3D2 (A-A-D-A-D) or A3BD (A-A-B-A-D) stoichiometry. We compared these receptor models in ligand free forms or as complexes with the natural agonist serotonin or with the anti-emetic antagonist granisetron. The 5-HT bound models of the 5-HT₃AD receptor complex display similar conformations at transmembrane and intracellular domains. However, granisetron-bound models resemble those obtained in ligand free conditions with transmembrane domains of the 5HT3D subunit showing similar conformational changes to 5HT3A subunits. Non-synonymous SNP rs6443930 (Gly 110 - Ala/Val/Asp) substitutions in the D subunit models revealed significant changes in the extracellular domain providing molecular evidence for the association of these SNPs with certain clinical disorders. Together, these data deepen our understanding of how the 5-HT3D subunit influences the gating mechanism of 5-HT₃ receptors under ligand binding.