Table 1.
Values of parameters for sequence exclusion criteria.
Fig 1.
Venn diagram summarising the number of 5-HT3 receptor A, B, C, D and E subunit sequences identified in different phyla from the animal kingdom. A detailed breakdown of subunit distribution is listed in S2 Table. The figure contains the numbers of B, C, D and E subunits for those species that also contain subunit A, thus our dataset by definition contained zero (0) sequences with only B, C, D, or E subunits.
Fig 2.
Phylogenetic tree of 5HT3A homolog proteins from animal phyla.
The colours of the species in the tree correspond to the colours of the phyla in the figure legend: Chordata (green with the human sequence highlighted with amber background), Nematoda (dark red), Arthropoda (orange), Platyhelminthes (dark purple), Mollusca (cyan), Rotifera (yellow), Tardigrada (maroon), Hemichordata (purple), Orthonectida (pale green), Echinodermata (teal), Annelida (blue) and Cnidaria (grey). This analysis involved 494 amino acid sequences. There was a total of 292 alignment positions in the final dataset. Evolutionary analyses were conducted in MEGA X and tree editing was performed in iTOL. Tree scale represents the number of differences between sequences.
Fig 3.
Homology models of heteromeric 5-HT3AE receptors (a) Extracellular view showing 5-HT3AE receptor heteromer formed with three A (maroon) subunits and two E (green) subunits with AAEAE stoichiometry (based on the AABAB stoichiometry [114]) where A+A- interface (ligand binding region) is indicated. (b) The A+A- extracellular interface of two adjacent subunits (principal subunit (A+) and complementary subunit (A-)) highlighting the six loops that converge to form the ligand binding site. Only two of the five subunits have been shown for ease of viewing. c) The loops in the principal subunit (loop A (cyan), B [115], C (pink)) and the complementary subunit (loops D (red), E (yellow), F (blue)) and the critical amino acid residues participating in the binding site are labelled. Human 5HT3A and 5HT3E subunit tertiary structures modelled using information from mouse 5HT3A receptor structures with PDB 6np0.1 [74] and PDB 6w1m.1 respectively by Swiss modelling software [94] and further edited in by UCSF Chimera software [116]. Residue numbers of the human 5HT3A (AAP35868.1) subunit (Fig 4) are used as the comparator in the following sections. Each 5HT3A subunit contains an extracellular N terminal helix (M1-P21 residues) signal peptide that helps in receptor translocation to the plasma membrane [117, 118]. The remainder of the extracellular region contains multiple beta strands with the orthosteric ligand binding site formed by β1 – β10 strands and six loops (T87-K239) followed by the signature Cys-loop (C163-C177) [97]. This sequence then leads into the four sequential transmembrane (TM) domains: TM1 (V252-L272), TM2 (R279-D299), TM3 (C318-K338) and TM4 (K457-W478). The intracellular loop (ICL) between TM3-TM4 (L341-L455) is involved in channel gating activities [40, 119, 120]. Resistance to inhibitors of cholinesterase 3 (RIC-3) a chaperone protein binds to the RIC-3 binding region present in between TM3 and TM4 domains to help in receptor translocation to cell membranes [121–123].
Fig 4.
Amino acid sequence of the human 5HT3A subunit (AAP35868.1).
The Cys-loop is marked in salmon, the extracellular loops are labelled in blue and transmembrane (TM) domains are depicted in purple, RIC-3 binding region (RIC-3 BR) depicted in pink. Functionally important amino acids as described in Table 2 are highlighted in grey.
Table 2.
Human 5HT3A subunit (AAP35868.1) extracellular domain amino acid residues that participate in functional activity of the receptor.
Fig 5.
Consensus amino acid logos of 5HT3A subunit regions derived from 449 different animal species.
Human 5HT3A subunit tertiary structure is modelled using information from PDB 6np0.1 using Swiss modelling [94] software and edited in UCSF Chimera software [116]. Sequence logos of loops A to F, TM domains and Cys-loop represented according to Table 2 and Figs 4 and S6 and S7.