Fig. 3: Odorant binding site of OR52cs.
From: Understanding the molecular mechanisms of odorant binding and activation of the human OR52 family
a Comparison of ligand-binding sites in OR52cs, OR51E2, and non-olfactory class A GPCRs. Agonists bound to OR51E2 (PDB: 8F76), β2-adrenergic receptor (PDB:3SN6), dopamine D2 receptor (PDB:6VMS), and μ-opioid receptor (PDB:6DDF) are shown as yellow, cyan, orange, and gray sticks, respectively, and OCA are shown as pink sticks. The orthosteric ligand-binding site and OCA binding site are indicated by blue ellipse and purple square, respectively. The OR52cs structure is shown in cartoon representation, and TM6 and TM7 are removed in the side view on the left panel for clarity. b OCA and its interacting residues within 4.5 Å of OCA are shown as sticks, and the Cα atom of Gly is represented as a green ball. The polar interactions are indicated as dashed blue lines (left). The interaction between OCA and OR52cs was analyzed and visualized using LigPlot+ v.2.2.7 (middle). Sequence conservation of the residues constituting the odorant binding pocket in the human OR52 family, OR51 family, and whole ORs is depicted using WebLogo 3 (right). c Structural alignment of OR52cs with OR51E2. OR51E2 is shown as light-gray, and PPI is shown as a yellow stick. Residues within 4.0 Å of the odorants are shown as sticks. d Dose-dependent cAMP response curves of OR52cs (black) and mutants by OCA treatment. The EC50 values for each curve are summarized in Supplementary Table 3. The mean ± S.E.M. from n = 5 independent experiments (OR52cs) and n = 3 independent experiments (mutants) are shown as symbols and error bars, respectively. e All-atom MD simulations of the OCA–OR52cs–Gs system. The distances between OCA and R2656.59, F2616.55, and I2085.46, respectively, were plotted over the 1 µs simulation time for five replicas.
