Fig. 1: The structure of xlσ1Rclosed-endo compared to hσ1RPD144418.
From: An open-like conformation of the sigma-1 receptor reveals its ligand entry pathway
a The structure of the hσ1RPD144418 (PDB: 5HK1) homotrimer is viewed parallel to the membrane, with two protomers rendered in the surface mode and one in the cartoon. The helices are rendered as cylinders, and are labeled as α1–α5 from the amino- (N-) to the carboxy- (C-) terminus throughout the paper. The cupin-fold domain is rendered as a blue β barrel, with the red sheets indicating the hydrogen bonds to disrupt for ligand entry as suggested previously20. The C-terminal two-helix bundle (α4/α5) is colored in green, while the N-terminal part is orange. The relative position of the ER membrane is indicated by two gray lines. b The close-up view of one protomer from panel (a). The bound ligand, PD144418, is displayed as magenta sticks. The two pathways proposed for ligand entry are indicated by two magenta arrows, PATH1 and PATH2. c Left, superposition of the xlσ1Rclosed-endo trimer (in green) and the hσ1RPD144418 trimer (in brown) viewed perpendicular to the membrane from the cupin-fold side. Right, superposition of one xlσ1Rclosed-endo protomer and one hσ1RPD144418 protomer viewed parallel to the membrane. d One xlσ1Rclosed-endo protomer is rendered in both cartoon and surface modes in a “slab” view, in which the internal cavity is displayed as a gray shadowy compartment within the β barrel. The purple mesh shows the simulated annealing Fo–Fc map contoured at 3.0 σ level corresponding to an unidentifiable molecule.
