Fig. 6: Crystal structure of HeimdallR1 and the docking of lutein and fucoxanthin using QM/MM simulations.
From: Structural insights into light harvesting by antenna-containing rhodopsins in marine Asgard archaea
a,b, Overall structure of HeimdallR1 with the retinal chromophore, viewed from the membrane plane (a) and the intracellular side (b). c,d, Fenestrations in HeimdallR1 (c) and Kin4B8-xanthorhodopsin (PDB ID: 8I2Z) (d). e, Conservation of the residues surrounding the fenestrations in HeimdallRs and Kin4B8-xanthorhodopsin. Glycine (G) and tyrosine (Y) are coloured orange and cyan, respectively, while polar [threonine (T), serine (S)] and hydrophobic [valine (V), isoleucine (I), leucine (L), alanine (A)] residues are coloured green and blue, respectively. f–h, HeimdallR1 structure, energy minimized using the hybrid QM/MM method (f), and the docking of lutein (g) and fucoxanthin (h) along the outer surface of TM6. Black dashed lines indicate hydrogen bonds. i, Zeaxanthin-bound Kin4B8-xanthorhodopsin (PDB ID: 8I2Z). See Extended Data Fig. 9 for zoom-in on the fenestration area.
