The Clash The Singles 2007 Rar [REPACK]
Both LBDs adopt the canonical agonist-bound (active) conformation with the C-terminal activation helix H12 sealing the ligand binding pocket (LBP) and the coactivator peptide bound to the surface generated by helices H3, H4 and, H12 (Figure 7A,B). LG754 ligands could be precisely placed in their respective electron density in the two LBDs as shown by the experimental omit electron density maps (Supplementary Figure S1), confirming that LG754 can bind to both RXR and RAR. The crystal of LG754-bound RARβ LBD contains two complexes in the asymmetric unit and, while the two RARβ molecules superpose very well (rsmd = 0.410 on 201 Cα) (Figure 7C), LG754 adopts a different conformation in each of them (Supplementary Figures S1B,C and S2). In both cases, LG754 is stabilized in the RARβ LBP through extensive van der Waals contacts and a network of ionic and hydrogen bonds between the carboxylate moiety of LG754, R269 in H5 and S280 in the β-turn (Figure 8A,B). However, the propoxy group of the ligand points either toward helices H6 and H7 (Figure 8A) or toward helix H12 (Figure 8B). Both ligand positions are compatible with an agonist conformation of RARβ LBD even though the orientation where the bulky group points toward H12 might destabilize slightly the active position of the activation helix, thus explaining why LG754 is not a full RAR agonist. Comparison of the LG754-bound RXRα LBD structure with that of the previously reported RXRα LBD bound to the full agonist CD3254  reveals some residue reorientations, the most significant one affecting L436 in helix H11 (Figure 8C). In the presence of CD3254, this leucine has a pivotal role in inducing the sharp turn on the LBP volume to accommodate the twisted ligand and in stabilizing the active conformation of H12. In contrast, our structure shows that L436 undergoes a significant conformational change and rotates toward H12 to accommodate the propoxy group of LG754. This conformer generates a steric clash with L455 from helix H12 accounting for the destabilization of the active conformation of H12 in solution. Such a mechanism has already been observed for the partial agonist UVI3002 , which displays a similar aliphatic extension projecting toward H12 (Figure 8D). In both cases, the bulky side chains act as antagonistic extensions, lowering the interaction strength between H12 and the LBD surface and accounting for the very weak agonistic profile of these ligands. This is in line with a previous crystal structure of RXRα in complex with LG754  showing a non-active RXRα LBD conformation with the C-terminal H12 flipping out to the solvent (Figure 7D). As already observed with 9CRA [70,71] (Figure 3A), LG754 is able to adopt an extended conformation in RARβ (Figure 9B,C) and a bent conformation in RXRα (Figure 9B,D). As a consequence, the tetrahydronaphtalene group of LG754 points toward helix H12 in RARβ, whereas, in RXRα, a rotation by about 90 around the C9-C10 orients the ring away from helix H12 (Figure 8).
the clash the singles 2007 rar
Structural basis of LG754 activity in RARβ and RXRα. (A,B) close-up view of LG754 in the LBP of RARβ as observed in the two molecules of the asymmetric unit. Side chains of residues in close contact with the ligand are shown as yellow sticks. In both cases, hydrogen bonds between the carboxylate group of LG754, R269 in H5 and S280 in the β-turn are highlighted in dashed black line. The propoxy group of the ligand points either toward helices H6 and H7 (in a) or toward helix H12 (in b); (C) close-up view of the superposition of RXRα LBP bound to LG754 (in green, PDB code 6sti) with RXRα LBP bound to CD3254 (in pink, PDB code 3fug) . The propoxy group of LG754 pointing toward H12 induces a reorientation of L436 from helix H11, as compared to its position in the RXRα-CD3254 complex, generating a steric clash with L455 of helix H12; (D) close-up view of the superposition of RXRα LBP bound to LG754 (in green, PDB code 6sti) with RXRα LBP bound to UVI3002 (in orange, PDB code 2p1v) . The aliphatic extension of UVI3002 induces the same positioning of L436 and L455, as observed in the structure of RXRα bound to LG754.