Supplementary Figure 1 Crystallization. a, Crystallization constructs of the ET B receptor are shown, with all of the modifications to the human wild-type the ET B receptor indicated. Residues interacting with both bosentan and K-8794 are colored green, the residue only interacting with bosentan is blue, and those only interacting with K-8794 are red, as shown in the figure. b, c, Effects of ET-1 on the release of AP-TGFα and antagonists on the ET-1-induced release of AP-TGFα in HEK293 cells expressing the endothelin receptors. In the competitive assays, the concentration of the agonist ET-1 was 0.2 nm, and the AP-TGFα release response in the ET-1 treatment alone was normalized to 100%. Symbols and error bars are means and s.e.m. (standard error of the mean), respectively. For most data points, the error bars are smaller than the symbols. d, e, Crystallographic data of the ET B -Y5-mT4L protein bound to K-8794 (d) and the ET B -Y4-mT4L protein bound to bosentan (e). The left panels show the crystals of the antagonist-bound ET B receptors. The middle and right panels show their crystal packings. T4L is shown as a grey cartoon, and the K-8794- and bosentan-bound ET B receptors are shown as orange and turquoise cartoons, respectively. Crystal lattices are indicated by black lines.
Supplementary Figure 2 Electron density. a, b, Fo Fc omit maps for K-8794 (a) and bosentan (b), contoured at 3.0 σ and 4.0 σ, respectively. TM6 and TM7 are omitted. c, The bosentan binding site, in which the colors represent the temperature factors ranging from 20 Å 2 (blue) to 120 Å 2 (red). d, Stereo view of the 2Fo Fc map, contoured at 1.0 σ, for the residues within 4 Å contact distances of the ligand in the K-8794-bound ET B structure. e,
Stereo views of the 2Fo Fc maps, contoured at 1.0 σ, for the residues within 4 Å contact distances of the ligand in the bosentan-bound ET B structure. f, Stereo view of the composite omit map, contoured at 1.0 σ, for the residues within 4 Å contact distances of the ligand in the bosentan-bound ET B structure.
Supplementary Figure 3 Comparison with other peptide-activated GPCRs. a c, Comparison of the antagonist binding sites of the peptide-activated GPCRs. Ribbon representations of the ET B receptor in complex with bosentan (a), Orexin receptor OX2 in complex with suvorexant (PDB accession number 4RNB) (b), and NOP receptor in complex with the peptidomimetic antagonist C-24 (PDB accession number 4EA3) (c) are aligned according to the position of Trp6.48, which is indicated by the stick model in each figure. The black dashed line indicates the position of the C atoms of Trp6.48. The smallmolecule antagonists are represented by stick models. Like the ET B receptor, OX2 belongs to the subfamily of the class A GPCRs, while NOP belongs to the subfamily. d, e, Electrostatic surfaces of the ET B structures bound to bosentan (d) and ET-1 (e), viewed from the extracellular side (left) and within the membrane plane (right). Bosentan and ET-1 are shown as sticks and transparent surfaces, colored blue and pink, respectively.
Supplementary Figure 4 Ligand-interaction diagrams. Interaction diagrams of K-8794 (a) and bosentan (b) with the ET B receptor. Interactions within 4 Å are shown. Polar and hydrophobic contacts are represented as red dashed and green lines, respectively.
Supplementary Figure 5 Homology between ET B and ET A. Amino acid sequence alignment of the human ET B (UniProt ID: P24530) and ET A (P25101) receptors. Secondary structure elements for -helices and -strands are indicated by cylinders and arrows, respectively. Conservation of the residues between ET A and ET B is indicated as follows: red panels for completely conserved, red letters for partially conserved, and black letters for not conserved. The residues involved in bosentan and K-8794 binding are shown as blue squares and orange diamonds, respectively.
Supplementary Figure 6 Small-molecule endothelin-receptor antagonists. Chemical structures of major small-molecule endothelin receptor antagonists. Endothelin receptor antagonists commonly have negatively-charged moieties (sulfonamide or carboxylate).
Supplementary Figure 7 Comparison of structural changes on ligand binding. a, b, Comparison of the ET-1 and bosentan binding modes, coloured as in Fig. 6. Receptors and ET-1 are represented by ribbons, and the side chains of ET-1 18-21 and bosentan are shown as sticks with transparent surfaces. c, The residues that interact with both ET-1 and bosentan are superimposed. d f, Comparison of the structural changes upon ET-1 (d), bosentan (e), and K-8794 (f) binding, coloured as in Figs. 1 and 4.
Supplementary note The different moieties between bosentan and K-8794 are located adjacent to the TM2 helix, in which the amino acid sequences are most divergent between the ET A and ET B receptors (Fig. 3g). Especially, His150 2.53, which is involved in the direct interaction with K-8794, is substituted with tyrosine in the ET A receptor. Therefore, we first hypothesized that the specific interaction between K-8794 and TM2 is predominantly responsible for the ET B-selectivity of K- 8794. However, the His150Tyr mutation did not alter the affinity for either bosentan or K-8794 (Table 1b). In contrast, the mutation to a smaller side chain (His150Ala) greatly reduced the affinities for both bosentan and K-8794, although His150 2.53 is not involved in any direct interactions with bosentan (Table 1b and Fig 3c). Considering that the K-8794-bound structure was obtained with the construct containing the thermostabilizing mutant Asp154Ala, it is possible that this mutation slightly affects the shape of the binding pocket, by disrupting the electrostatic interaction between Asp154 2.57 and His150 2.53, which is actually observed in the bosentan-bound structure. These data suggest that the interaction between K-8794 and His150 2.53 is not important for receptor binding, while His150 2.53 facilitates the binding of these antagonists by narrowing the shape of the binding pocket, rather than by forming any direct interactions. This is consistent with the previous mutation analysis of the ET A receptor, which showed that the bulky residue at position 2.53 is important for bosentan binding 1. 1 Webb, M. L. et al. Mutational analysis of the endothelin type A receptor (ETA): interactions and model of selective ETA antagonist BMS-182874 with putative ETA receptor binding cavity. Biochemistry. 35, 2548-2556, doi:10.1021/bi951836v (1996).