Basak S , Gicheru Y , Kapoor A , Mayer ML , Filizola M , Chakrapani S .

R01 GM108921 NIGMS NIH HHS , R01 GM131216 NIGMS NIH HHS , R35 GM134896 NIGMS NIH HHS , S10 OD018522 NIH HHS

	Fig. 1. Cryogenic electron microscopy (cryo-EM) structure of granisetron-bound full-length serotonin 3A receptor (5-HT3AR). a A schematic showing three fundamental conformations that constitute the gating cycle in pentameric ligand-gated ion channel (pLGIC) function: a resting state, a transient open state, and a desensitized state. Agonist-binding shifts the equilibrium towards the open state and then to the high-agonist affinity, desensitized state. Orthosteric (competitive) antagonists exert their effect by shifting the equilibrium towards the resting (or inhibited) state. b Trace showing a continuous recording of 5-HT3AR currents (−60 mV) in oocytes measured by two-electrode voltage clamp (TEVC) in the presence of serotonin (marked by red line) and pre-applied granisetron (marked by orange line). The effect of granisetron inhibition was fully reversible as seen in the third pulse. c Map of full-length 5-HT3AR-granisetron reconstructed from 46,757 particles at 2.92 å resolution. Side-view parallel to the membrane and extracellular view are shown in left and right panels, respectively. Each monomer is shown in a different color for clarity. Density corresponding to granisetron (left panel, circle) and glycans (right panel, arrow) are indicated. d Three-dimensional cartoon model of 5-HT3AR-granisetron structure generated from EM reconstruction (side view). For each subunit, three sets of glycans are shown as stick representation. e Top-view of 5-HT3AR-granisetron map sliced at the binding site to show all five granisetron molecules, each bound at the interface of two subunits (indicated by arrows)
	Fig. 2. The granisetron binding site. a The density map of granisetron contoured at 9σ (left) and map around the residues at the binding site located at the intersubunit interface (right). The residue labels on the principal subunit are marked in black and those on the complementary subunit are marked in brown. b A comparison of the serotonin 3A receptor-apo (5-HT3AR-apo), 5-HT3AR-granisetron, and 5-HT3AR-serotonin structures shows that residues involved in ligand-binding undergo rotameric reorientation. c Alignment of the three structures reveals an inward motion of loop C in 5-HT3AR-granisetron relative to 5-HT3AR-apo, which is in the direction toward activation as seen in the 5-HT3AR-serotonin structure
	Fig. 3. Conformational differences between the apo and ligand-bound states. a An extracellular view of the extracellular domain (ECD) upon global alignment of serotonin 3A receptor-apo (5-HT3AR-apo) structure with 5-HT3AR-granisetron (left) and 5-HT3AR-serotonin (right). Only ECDs from two non-adjacent subunits is shown for clarity. A counter-clockwise motion of the ECD is observed as indicated by the arrows. The serotonin-induced motion is of larger magnitude compared to that of granisetron, highlighted by the solid and dotted arrows, respectively. b A comparison of the transmembrane domains (TMDs) (viewed from the extracellular side) in 5-HT3AR-granisetron structure (left) and 5-HT3AR-serotonin (right) when aligned with respect to 5-HT3AR-apo. Only two non-adjacent TMD subunits are shown for clarity. In both panels, a clockwise rotation of the TMD is observed with 5-HT3AR-serotonin revealing a larger change. c Pathway of ion permeation of 5-HT3AR-apo and 5-HT3AR-granisetron generated with HOLE54. The cartoon representation of two subunits are shown for clarity. The locations of pore constrictions are shown as sticks. The pore radius is plotted as a function of distance along the pore axis. The dotted line indicates the approximate radius of a hydrated Na+ ion, which is estimated at 2.76 å (right)35
	Fig. 4. Assessment of the overall stability of the granisetron-serotonin 3A receptor (5-HT3AR) structure. a Time evolution of the root mean squared deviations (RMSD) of Cα atoms of secondary structure elements of the extracellular domain (ECD) and all Cα atoms of the 5-HT3AR pentamer (left panel). The RMSD of each of the granisetron molecules (labeled CWB) in each subunit A to E (right panel) calculated with respect to the cryo-EM-derived structure during 100 ns production simulations. b Two possible granisetron poses with the bicyclic ring in boat/chair or chair/chair conformation and the N-methyl group in axial or equatorial positions in the piperidine chair conformation. These two poses were used as input for metadynamics-based ranking. c Ranking of the two granisetron poses shown in b using metadynamics. Error bars represent the standard error of the mean of RMSD estimates from 10 metadynamics simulations. Source data are provided as a Source Data file.
	Fig. 5. Effects of mutations at the ligand-binding pocket on granisetron inhibition. a Granisetron interactions with Trp156 and Tyr207 from the principal subunit and Trp63, Arg65, Tyr126 from the complementary subunit are depicted as stick representation. b Serotonin dose response measured by two-electrode voltage clamp (TEVC) recordings (at −60 mV) for wild-type (WT) 5-HT3AR, W63Y, R65A, Y126F, W156Y, and Y207F mutants, expressed in oocytes. The half-maximal effective concentration (EC50), the Hill coefficient (nH), and the number of independent oocyte experiments for WT and mutants are: WT (EC50: 2.70 + 0.09 μM; nH: 2.3 + 0.17; n: 3), W63Y (EC50: 9.93 + 0.77 μM; nH: 3.1 + 0.72; n: 4), R65A (EC50: 13.79 + 0.50 μM; nH: 4.4 + 0.59; n: 4), Y126F (EC50: 42.8 + 4.4 μM; nH: 2.6 + 0.71; n: 4), W156Y (EC50: 306 + 44 μM; nH: 1.58 + 0.24; n: 4), and Y207F (EC50: 20.35 + 1.7 μM; nH: 1.9 + 0.27; n: 5). c Currents were elicited in response to serotonin (concentrations used near EC50 values of WT and mutants). The following concentrations of serotonin were used: WT-1 μM, W63Y-10 μM, R65A-10 μM; Y126F-40 μM, W156Y-200 μM, and Y207F-20 μM. Currents were measured in response to serotonin (marked by red line) and pre-application of granisetron (marked by orange line). Dotted arrows show the extent of granisetron inhibition. d A plot of the ratio of peak current in the presence of granisetron to peak current in the absence of granisetron is shown for WT and mutants. Data are shown as mean ± s.d. (n is indicated within parentheses). Significance at p = 0.001 (***) and p = 0.05 (**) calculated by two-sample t test for WT and mutants. Source data are provided as a Source Data file
	Supplementary Figure 1. Effect of 100 nM granisetron on 5-HT3AR currents. TEVC recordings (at -60mV) for wild type 5-HT3AR in the presence of 10 µM serotonin, upon preapplication of 100 nM granisetron, and co-application of 10 µM serotonin and 100 nM granisetron.
	Supplementary Figure 2. Sequence of mouse 5-HT3AR used in the cryo-EM study. Full length mouse 5-HT3AR sequence used in the cryo-EM study. The sequence also includes strep-tags (green), linker regions (blue), TEV cleavage site (gray), and 1D4-tag (yellow). Secondary structural elements are indicated above the sequence. Regions in the M3-M4 linker indicated in gray color are not seen in the final refined structure. Glycosylation sites are marked as blue arrows. Key residues involved in serotonin binding sites are highlighted in brown color. Cysteines present in the cys-loop are shown as cyan color. Pore-facing residues in M2 are shown in green color. Arg416 in the ICD is shown in red.
	Supplementary Figure 3. Data Processing workflow. A schematic representation of the steps followed in data processing leading to 2.92 Ã reconstruction. Classes within the box used for further processing.
	Supplementary Figure 4. Estimation of resolution and validation of the models. a. A representative micrograph of 5-HT3AR incubated with 100 μM granisetron in vitreous ice (left). 2D classes showing various orientations used for 3D reconstruction (right). b. Fourier shell correlation curves before (red) and after (blue) the mask application in RELION. The dashed line indicates FSC of 0.143. c. For validation, FSC curves of the refined model versus summed map, refined model versus half map 1 (used for refinement), and refined model versus half map 2 (not used for refinement) were calculated. d. Different views of local resolution of 5-HT3ARgranisetron reconstruction was estimated using the ResMap program.
	Supplementary Figure 5. Map correlation of granisetron-5-HT3AR structure. Validation of the various regions of the model (shown in stick representation) and corresponding density map (mesh) around the residues are shown here. Residues are represented as sticks. The depicted regions in 5-HT3AR-granisetron and the corresponding contour levels: Cys loop (8.2 σ), loop C (8.2 σ), loop F (8.0 σ), M2 (8.2 σ), M2-M3 (6.5 σ), M4 (8.2 σ), MX helix (8.0 σ), and MA helix (8.2 σ). The boxed region highlights the cysteine disulfide-bridge in cys-loop.
	Supplementary Figure 6. Structural differences between granisetron and tropisetron binding poses in 5-HT3AR and AChBP structures. a. In the 5-HT3AR-granisetron structure, the indazole ring in granisetron lies flat in the binding site allowing for a potential cation-pi stacking interaction between Arg65, granisetron and Trp168 in loop F. b. In the 5-HT3AR-tropisetron structure1, the indole ring is tilted upwards (by 86.2º with respect to granisetron, measured at C12-C14 bond). Trp168 sidechain is tilted away from the binding site and Arg65 may adopt a different rotameric orientation (although the density for this region is not clear). c. The granisetron-binding pose in the AChBP-5-HT3AR chimeric mutant2. Positions equivalent to R65 and W168 in 5-HT3AR are shown. d. The tropisetron-binding pose as seen in the structure of AChBP crystal structure3. Positions equivalent to R65 and W168 in 5-HT3AR are shown.
	Supplementary Figure 7. Alignment of apo and ligand-bound structures of 5-HT3AR. An alignment of 5-HT3AR-apo, 5-HT3AR-granisetron, 5-HT3AR serotonin structures. a. A view of the ECDs from the extracellular end when aligned with respect to the TMDs. b. A view of the TMDs from the extracellular end when aligned with respect to the ECDs. The arrows show the putative direction of displacements among the three structures.
	Supplementary Figure 8. Molecular interactions between granisetron and ligand-binding residues during simulation. 5-HT3AR-granisetron interaction fingerprints calculated for each ligand-protein complex (labelled CWB_A-CWB_E) from 100 ns production simulations. Nine interaction types are calculated: apolar (hydrophobic), face-to-face aromatic (Aro_F2F), edge-toface aromatic (Aro_E2F), hydrogen bond with the protein as hydrogen bond donor (Hbond_ProD), hydrogen bond with the protein as hydrogen bond acceptor (Hbond_ProA), electrostatic with the protein positively charged (Elec_ProP), electrostatic with the protein negatively charged (Elec_ProN,), one-water mediated and two-water mediated hydrogen bond interactions. Ligandprotein interactions are limited to those formed with 5-HT3AR side chains. Only interactions with average probability above 5% are displayed.
	Fig. 1. Cryogenic electron microscopy (cryo-EM) structure of granisetron-bound full-length serotonin 3A receptor (5-HT3AR). a A schematic showing three fundamental conformations that constitute the gating cycle in pentameric ligand-gated ion channel (pLGIC) function: a resting state, a transient open state, and a desensitized state. Agonist-binding shifts the equilibrium towards the open state and then to the high-agonist affinity, desensitized state. Orthosteric (competitive) antagonists exert their effect by shifting the equilibrium towards the resting (or inhibited) state. b Trace showing a continuous recording of 5-HT3AR currents (−60 mV) in oocytes measured by two-electrode voltage clamp (TEVC) in the presence of serotonin (marked by red line) and pre-applied granisetron (marked by orange line). The effect of granisetron inhibition was fully reversible as seen in the third pulse. c Map of full-length 5-HT3AR-granisetron reconstructed from 46,757 particles at 2.92 Å resolution. Side-view parallel to the membrane and extracellular view are shown in left and right panels, respectively. Each monomer is shown in a different color for clarity. Density corresponding to granisetron (left panel, circle) and glycans (right panel, arrow) are indicated. d Three-dimensional cartoon model of 5-HT3AR-granisetron structure generated from EM reconstruction (side view). For each subunit, three sets of glycans are shown as stick representation. e Top-view of 5-HT3AR-granisetron map sliced at the binding site to show all five granisetron molecules, each bound at the interface of two subunits (indicated by arrows)
	Fig. 2. The granisetron binding site. a The density map of granisetron contoured at 9σ (left) and map around the residues at the binding site located at the intersubunit interface (right). The residue labels on the principal subunit are marked in black and those on the complementary subunit are marked in brown. b A comparison of the serotonin 3A receptor-apo (5-HT3AR-apo), 5-HT3AR-granisetron, and 5-HT3AR-serotonin structures shows that residues involved in ligand-binding undergo rotameric reorientation. c Alignment of the three structures reveals an inward motion of loop C in 5-HT3AR-granisetron relative to 5-HT3AR-apo, which is in the direction toward activation as seen in the 5-HT3AR-serotonin structure

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