High-resolution model of Arabidopsis Photosystem II reveals the structural consequences of digitonin-extraction

In photosynthesis, solar energy is converted into stored chemical energy and oxygen. In higher plants, the photosynthetic process is performed and regulated by the Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. Using single-particle cryo-electron microscopy we obtained the first high-resolution structure of Arabidopsis PSII supercomplex (C2S2) at an average resolution of 2.79 A, enabling the first in-depth comparison to the two higher plant, Spinach and Pea, PSII structures published. The extrinsic proteins PsbP and PsbQ were not detected; the C-terminus of the D1 proteins was found to be disordered; and the expected site of the Mn4CaO5 exhibits a single metal ion density, reminiscent of an early stage of PSII photoactivation. Using digitonin detergent to extract PSII complexes, we demonstrate the importance of: the phosphatidylglycerol lipid (LHG2630) headgroup in the trimerization of the light-harvesting complex II; the digalactosyldiacylglycerol DGD520 in the stabilization of PsbJ subunit and its influence in the stabilization of CP43 loop E; the choice of detergent to maintain the integrity of membrane protein complexes. We suggest the underlying mechanisms that led to the disordered PsbO loops and propose that PsbW and PsbH subunits of opposite monomers participate in PSII dimerization. This structural study establishes an important atomic model for future studies of Arabidopsis Photosystem II while advising precaution in the choice of detergents for extraction of fully stable PSII complexes.