Extended Data Fig. 9: Structural features of Kin4B8.
From: Phototrophy by antenna-containing rhodopsin pumps in aquatic environments
a, Cryo-EM single-particle analysis of the zeaxanthin-bound Kin4B8. b, Comparison of the cryo-EM and crystal structures of Kin4B8. c, Cryo-EM density of the zeaxanthin, which allows unambiguous identification of the molecule. In particular, resolution of the half of zeaxanthin proximal to the fenestration is high enough to permit identification of the dimethyl group of its hydroxyl ring. d, Comparison of the oligomeric structures of Kin4B8, S. ruber XR (PDB ID: 3DDL), BR (PDB ID: 1C3W), GPR (PDB ID: 7B03). With the ECL1 sheet inside, Kin4B8 forms a hexamer with aligned directions to the membrane in the crystal packing. The pentameric structure would reflect a physiological condition, in contrast to the previously reported head-to-tail dimer of S. ruber XR. e, Structural comparison of Kin4B8 with S. ruber XR (PDB ID: 3DDL), bacteriorhodopsin (BR) (PDB ID: 1C3W), and GPR (PDB ID: 7B03), with root mean square deviations (RMSD) of 1.44, 1.96, and 2.61 Å, respectively. Notably, the N-terminal region (residues 6–11) and ECL1 form a 3-stranded antiparallel β-sheet, as in S. ruber XR and other omega rhodopsins. f, Key rhodopsin proton pump motifs in Kin4B8. Black dashed lines indicate hydrogen-bonding interactions. Red spheres indicate water molecules.
