Fig. 3

Crystal structure of the amphioxus NR7 ligand-binding domain (LBD). A, B Overall views from the front (A) and the back (B) of the LBD of NR7 depicted as green ribbons with corresponding helices indicated. NR7-specific features, such as the shortened helix H10 (called H10’) and the shortened helix H11 (called helix H11’) and the collapsed region connecting both helices are shown as orange ribbons. The C-terminal helix H12 is shown in red. C Zoom on the region of helices H3, H6, and H7 that differs markedly from the amphioxus RXR LBD structure (shown as grey ribbons), indicating a shortening of helix H3, an inwards movement of helix H6 and a straighter H7 helix as compared to RXR. The π-turn in RXR is indicated by an asterisk. D Enlarged view of NR7 ligand-binding pocket, showing that aromatic and hydrophobic residues fill the pocket and stabilize the apo conformation. E The loop H10’-H11’ makes stabilizing interactions with helix H7, with strong interactions between Phe356 and Tyr287 (H7), and with Asp241 (H5)