The heart of oxygenic photosynthesis is the water-splitting photosystem II (PSII), which forms supercomplexes with a variable amount of peripheral trimeric light-harvesting complexes (LHCII). Our knowledge of the structure of green plant PSII supercomplex is based on findings obtained from several representatives of green algae and flowering plants; however, data from a non-flowering plant are currently missing. Here we report a cryo-electron microscopy structure of PSII supercomplex from spruce, a representative of non-flowering land plants, at 2.8 Å resolution. Compared with flowering plants, PSII supercomplex in spruce contains an additional Ycf12 subunit, Lhcb4 protein is replaced by Lhcb8, and trimeric LHCII is present as a homotrimer of Lhcb1. Unexpectedly, we have found α-tocopherol (α-Toc)/α-tocopherolquinone (α-TQ) at the boundary between the LHCII trimer and the inner antenna CP43. The molecule of α-Toc/α-TQ is located close to chlorophyll a614 of one of the Lhcb1 proteins and its chromanol/quinone head is exposed to the thylakoid lumen. The position of α-Toc in PSII supercomplex makes it an ideal candidate for the sensor of excessive light, as α-Toc can be oxidized to α-TQ by high-light-induced singlet oxygen at low lumenal pH. The molecule of α-TQ appears to shift slightly into the PSII supercomplex, which could trigger important structure-functional modifications in PSII supercomplex. Inspection of the previously reported cryo-electron microscopy maps of PSII supercomplexes indicates that α-Toc/α-TQ can be present at the same site also in PSII supercomplexes from flowering plants, but its identification in the previous studies has been hindered by insufficient resolution.

Central European Institute of Technology Masaryk University Brno Czech Republic

Centre of the Region Haná for Biotechnological and Agricultural Research Department of Genetic Resources for Vegetables Medicinal and Special Plants Crop Research Institute Olomouc Czech Republic

Czech Advanced Technology and Research Institute Palacký University Olomouc Czech Republic

Department of Biophysics Faculty of Science Palacký University Olomouc Czech Republic

Department of Experimental Biology Faculty of Science Palacký University Olomouc Czech Republic

Institute of Biochemistry and Biotechnology Martin Luther University Halle Wittenberg Halle Saale Germany

Institute of Chemical Biology National Hallenic Research Foundation Athens Greece

Institute of Experimental Botany of the Czech Academy of Sciences Centre of Plant Structural and Functional Genomics Olomouc Czech Republic

Interdisciplinary Research Center HALOmem Charles Tanford Protein Center Martin Luther University Halle Wittenberg Halle Saale Germany

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