8IR5

XFEL structure of cyanobacterial photosystem II under dark conditions

8IR5 の概要

• エントリーDOI: 10.2210/pdb8ir5/pdb
• 分子名称: Photosystem II protein D1, Photosystem II reaction center protein K, Photosystem II reaction center protein L, ... (41 entities in total)
• 機能のキーワード: psii, photosystem ii, xfel, photosynthesis
• 由来する生物種: Thermostichus vulcanus; 詳細
• タンパク質・核酸の鎖数: 39
• 化学式量合計: 724492.48

構造登録者

Li, H.,Suga, M.,Shen, J.R. (登録日: 2023-03-17, 公開日: 2024-01-17, 最終更新日: 2024-11-13)

主引用文献

Li, H.,Nakajima, Y.,Nango, E.,Owada, S.,Yamada, D.,Hashimoto, K.,Luo, F.,Tanaka, R.,Akita, F.,Kato, K.,Kang, J.,Saitoh, Y.,Kishi, S.,Yu, H.,Matsubara, N.,Fujii, H.,Sugahara, M.,Suzuki, M.,Masuda, T.,Kimura, T.,Thao, T.N.,Yonekura, S.,Yu, L.J.,Tosha, T.,Tono, K.,Joti, Y.,Hatsui, T.,Yabashi, M.,Kubo, M.,Iwata, S.,Isobe, H.,Yamaguchi, K.,Suga, M.,Shen, J.R.
Oxygen-evolving photosystem II structures during S 1 -S 2 -S 3 transitions.
Nature, 626:670-677, 2024

PubMed Abstract: Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of S states (i = 0-4) at the MnCaO cluster, during which an extra oxygen (O6) is incorporated at the S state to form a possible dioxygen. Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). Y, a tyrosine residue that connects the reaction centre P680 and the MnCaO cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O-O bond formation.

PubMed: 38297122
DOI: 10.1038/s41586-023-06987-5

実験手法

X-RAY DIFFRACTION (2.15 Å)