High resolution structure of plant Light-Harvesting Complex II (LHCII) provides insight into lutein conformations and energy quenching

Plant Light Harvesting Complex II (LHCII) is found in the thylakoid membranes of chloroplasts and balances two roles: energy collection for photosynthesis and energy dissipation to prevent photo-damage when there is excessive sunlight. The mechanism for LHCII to switch between two energetic states has been debated but may involve a pH-triggered conformational change. Here we present single-particle cryo-electron microscopy (EM) structures of "light-harvesting" LHCII in detergent at pH 7.5 and pH 4.5. The high resolution (2.48 [A]) maps provide clear placements for all bound pigments, giving high confidence in the models. Surprisingly, we find that there is little conformational change to the polypeptide between these new light harvesting structures and previously published crystals structures, thought to be energy dissipating. The crossing angles of helix A/B and the Lutein 1-Chlorophyll 612 separation distances are similar. This contrasts with other recent analyses of LHCII by single-particle EM that suggested a change to the helix A/B angle and a reduction in Lutein 1-Chlorophyll 612 separation may trigger quenching and a photoprotective state. The high resolution of our structures also allowed us to investigate small conformational changes of the lutein within L1/L2 binding sites of LHCII, revealing rotations and distortions in the pigment that could lead to changes in energy transfer. In addition, we find that low pH causes LHCII to form a destabilised structure where pigment loss from the V1 binding site (usually violaxanthin or zeaxanthin) correlated with a disordered C-terminus, often for just one LHCII monomer with an LHCII trimer. Overall, our findings have important implications for the molecular mechanism of photoprotection.