Figure 1
Mutual orientation of Cars and their closest co-facial Chl partners in the L1/L2 sites. (a–c) Positioning of Lhcb1 within the membrane (PDB: 3JCU)9. The views are along the membrane plane (a,b) and from the stromal side (c). A close-up view of the L1/L2 sites in b shows the pigment pairs and the naming nomenclature according to Liu et al.7. Transmembrane helices A, B, C and amphipathic helices D and E are shown in light-blue. The remaining pigment composition of Lhcb1 is shown in c: 8 Chl a’s are shown in green, 6 Chl b’s are in red, Vio and neoxanthin are shown in pink and yellow, accordingly (molecules and proteins plotted with VMD31). (d) The full trimer of the LHCII antenna (lumenal view). Monomers are emphasized by colors. (e,f) Superposition of all the L1 and L2 pairs from Lhcb1-5 and Lhca1-4 protein units. The front view (e) and the side view (f) also show the coordinate system associated with the Chl. Cars are shown as ghost atoms to emphasize the distribution rather than the actual positions, except for Lut 620 from L1 site of Lhcb1 which is highlighted for comparison. Only Chl a612 from the L1 site of Lhcb1 represents all the Chls for clarity because the other Chls from the pairs largely differ only by the conformation of their phytol tails, which do not contribute to the transition density (Supplementary Fig. 1a).
