Fig. 3

Fig. 3 Cryo-EM structure of DrOTOP1 with inhibitor C2.2.

A Top and B side views of cryo-EM structure of DrOTOP1 complexed with C2.2 (DrOTOP1_C2.2), with one monomer colored purple (N-domain) and plum-pink (C-domain), the other monomer colored light gray, bound-lipids colored tan, small molecules colored cyan, and the nanodisc micelle shown as a transparent surface. C Inset of (B) zoomed on the C-domain pocket with the model colored in plum-pink and cryo-EM map shown as a gray transparent surface. D Same view and coloring as (C) showing DrOTOP1_C2.2 in comparison with the apo structure of DrOTOP1 (DrOTOP1_apo) (PDB:6NF4) superimposed and shown as a transparent light green stick and cartoon, with pocket-lining residues labeled. E Side views of DrOTOP1_apo (left) and DrOTOP1_C2.2 (right) models with only the cryo-EM density of cholesterol lipids (tan) and inhibitor C2.2 (cyan) near the outer site shown. Insets show density found in the outer site as a transparent surface, cholesterol (tan) and with C2.2 (cyan) models shown as sticks. Gray rectangles indicate the height of the lipid bilayer, with the extracellular side (Ext.) on top and the intracellular side (Int.) below. F 90° rotated view of models as (E), showing cryo-EM densities of cholesterol lipids (tan) and C2.2 (cyan) near the central site. Insets show density found in the central site as a transparent surface, with cholesteryl hemisuccinate (CHS) (tan) and C2.2 (cyan) shown as sticks. G View of outer sites showing a superimposed comparison of DrOTOP1_C2.2 with bound C2.2 and DrOTOP1_apo with bound cholesterol (CLR), with DrOTOP1_apo shown as transparent stick and cartoon, highlighting conformational differences. Movement of TM3 is indicated (red arrow). H Bottom view of DrOTOP1_C2.2 and DrOTOP1 superimposed, with C2.2 models shown as cyan spheres. Movement of TM3 and TM9 indicated with red arrows, and movement of TM6 indicated with a black arrow. I Similar view as (G) for the central site, with C2.2 and CHS shown in the central site, highlighting conformational changes. Movement of TM6 (black arrow) and TM9 (red arrow) are indicated.