Fig. 1: Phylogeny of NDQ rhodopsins.

a Phylogenetic tree of the NDQ rhodopsins clade. Subgroups 1 and 2 are highlighted in green and blue, respectively. b Sequence alignment of the key regions of the representative NDQ rhodopsins: internal polar/rechargeable amino acid residues (left), functionally and structurally relevant external amino acid residues (right). For the representative NDQ rhodopsins we selected biophysically characterized proteins also described in²². The key positions are marked with bold numbers according to the KR2 sequence. Additional RSB counterion (E64 in ErNaR) in the Subgroup 2 is highlighted red. Additional positively charged residue near the interprotomeric sodium binding site (R19 in ErNaR) is highlighted blue. c Overall side view of the KR2 protomer (PDB ID: 6YC3¹⁹). Putative sodium translocation pathway is shown with a black arrow. Helices are indicated with bold capital letters (A-G). Hydrophobic/hydrophilic membrane core boundaries are shown with gray horizontal lines. d The RSB region of KR2 in the ground (left, yellow, PDB ID: 6YC3¹⁹) and O (right, blue, PDB ID: 6XYT¹⁹) states of the photocycle and the role of L74. Distance from L74 to the nearest water molecule in the Schiff base cavity is indicated with a red arrow (left) and is given in bold italic. The flipping motion of the L74 side chain upon sodium binding in the O state is also indicated with a red arrow (right). The sodium ion is shown with the purple sphere. e Interprotomeric sodium binding site in KR2 (PDB ID: 6YC3¹⁹). Overall view of the KR2 pentamer from the extracellular side (left) and detailed view of the site (right). Two neighboring protomers are colored yellow and green. The BC loop is colored dark blue. The sodium ion (purple sphere) coordination is indicated with black dashed lines.