9Z69

RT XFEL structure of the one-flash state of Photosystem II (1F, S2 rich) at 1.98 Angstrom obtained from conventional data at 9.5 keV

This is a non-PDB format compatible entry.

Summary for 9Z69

• Entry DOI: 10.2210/pdb9z69/pdb
• Descriptor: Photosystem II protein D1 1, Photosystem II reaction center protein K, Photosystem II reaction center protein L, ... (36 entities in total)
• Functional Keywords: water oxidation, photosynthesis, manganese cluster, bioenergy
• Biological source: Thermosynechococcus vestitus BP-1; More
• Total number of polymer chains: 40
• Total formula weight: 765519.14

Authors

Bhowmick, A.,Kern, J.,Yano, J.,Yachandra, V.K.,Minnetian, N.M.,Zhang, M. (deposition date: 2025-11-14, release date: 2026-08-26, Last modification date: 2026-09-16)

Primary citation

Bhowmick, A.,Zhang, M.,Simon, P.S.,Makita, H.,Nangca, I.I.,Szilagyi, E.,Kretzschmar, M.,Doyle, M.D.,Minnetian, N.M.,Hussein, R.,Hart, O.,Chatterjee, K.,Aydin, A.O.,Shevela, D.,Cheah, M.H.,Croy, N.,Chernev, P.,Fransson, T.,Tiwari, V.,Sanchez, H.,Schleissner, P.,Lemons, R.,Gate, G.,Henstridge, M.,Glownia, J.M.,Poitevin, F.,Rosenberg, D.J.,Dehe, S.,Gee, L.B.,Tono, K.,Owada, S.,Oggenfuss, R.,Ozerov, D.,Sander, M.,Mankowsky, R.,Lemke, H.T.,Young, I.D.,Holton, J.M.,Mittan-Moreau, D.W.,Paley, D.W.,Afonine, P.V.,Moriarty, N.W.,Adams, P.D.,Mamedov, F.,Dobbek, H.,Zouni, A.,Alonso-Mori, R.,Bergmann, U.,Brewster, A.S.,Sauter, N.K.,Messinger, J.,Kern, J.F.,Yachandra, V.K.,Yano, J.
An additional water is introduced into the manganese cluster during the formation of the S 3 state of photosystem II.
Nat Commun, 17:-, 2026

PubMed Abstract: During photosynthetic water oxidation, the MnCa cluster in Photosystem II progresses through five intermediate S (i = 0-4) states. X-ray crystallography studies have reported the insertion of one new O ligand during the formation of the S state, but recent studies question the presence of this additional ligand based on cryo-EM and earlier room-temperature crystallography data. There is also controversy about whether the O-O bond interaction already occurs in the S state or in the subsequent S to S transition. Here we report conventional high-resolution data for the S, S, and S states to a resolution of ~1.9 Å, and anomalous diffraction data at two energies (9.5 keV and 7 keV), that was used to model the Mn positions, followed by determination of oxygen positions using the high-resolution maps. We show that the new oxygen atom, O (or O6), in the S state is observable as a distinct peak without any restraints, confirming its ligation to Mn1 and Ca. The O-O5 distance is ~2.1 Å, supporting no strong interaction between them in the S state, suggesting that if this is the O-O bond formation site, it is formed during the S to S transition initiated by the final oxidation of the cluster.

PubMed: 42632826
DOI: 10.1038/s41467-026-76805-9

Experimental method

X-RAY DIFFRACTION (1.98 Å)