Figure 7. Proton transfer pathways of V. radiata CIV.
VrCOX1 (transparent ribbon), co-factors (stick) and key residues (colored stick) are shown for the D channel (yellow), K channel (purple) and H channel (green). Proton-channel residues that are mutated in V. radiata with respect to B. taurus are marked with an asterisk (*). Approximate position of matrix and IMS ends of the transmembrane region are shown.
Figure 7—figure supplement 1. Sequence alignment of COX1 highlighting the H, D and K channels.
COX1 sequences from V. radiata (Vr), Arabidopsis thaliana (At), S. cerevisiae (Sc), and B. taurus (Bt) were aligned with Clustal Omega. Proton pathway residues are highlighted: D channel in yellow, H channel in green and K channel in purple. Proton-channel residues that differ between V. radiata and B. taurus are marked with an arrow of the same color as the channel to which the residue belongs. Boxes indicate α-helices in the VrCOX1 atomic model. Key residues are marked with arrows: heme a-coordinating residues in blue, heme a3-coordinating residues in orange, CUB-coordinating residues in magenta. RNA-editing sites are marked with gray arrows, see also Supplementary file 1d. The HPEVY ring is bolded. Symbols underneath aligned residues: * fully conserved, : conservation between group of strongly similar properties, . conservation between group of weakly similar properties.