8IRA

XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 200-microsecond delay

Summary for 8IRA

• Entry DOI: 10.2210/pdb8ira/pdb
• Descriptor: Photosystem II protein D1, Photosystem II reaction center protein K, Photosystem II reaction center protein L, ... (41 entities in total)
• Functional Keywords: psii, photosystem ii, xfel, photosynthesis
• Biological source: Thermostichus vulcanus; More
• Total number of polymer chains: 39
• Total formula weight: 724492.48

Authors

Li, H.,Suga, M.,Shen, J.R. (deposition date: 2023-03-17, release date: 2024-01-17, Last modification date: 2024-11-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.2 Å)