4UB8

Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser

Summary for 4UB8

• Entry DOI: 10.2210/pdb4ub8/pdb
• Related: 4UB6
• Descriptor: Photosystem Q(B) protein, Photosystem II reaction center protein K, Photosystem II reaction center protein L, ... (41 entities in total)
• Functional Keywords: photosynthesis, electron transport, oxygen evolution, water splitting, photo system ii
• Biological source: Thermosynechococcus vulcanus; More
• Total number of polymer chains: 39
• Total formula weight: 729499.60

Authors

Suga, M.,Akita, F.,Hirata, K.,Ueno, G.,Murakami, H.,Nakajima, Y.,Shimizu, T.,Yamashita, K.,Yamamoto, M.,Ago, H.,Shen, J.R. (deposition date: 2014-08-12, release date: 2014-12-03, Last modification date: 2024-10-23)

Primary citation

Suga, M.,Akita, F.,Hirata, K.,Ueno, G.,Murakami, H.,Nakajima, Y.,Shimizu, T.,Yamashita, K.,Yamamoto, M.,Ago, H.,Shen, J.R.
Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses.
Nature, 517:99-103, 2015

PubMed Abstract: Photosynthesis converts light energy into biologically useful chemical energy vital to life on Earth. The initial reaction of photosynthesis takes place in photosystem II (PSII), a 700-kilodalton homodimeric membrane protein complex that catalyses photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been solved by X-ray diffraction (XRD) at 1.9 ångström resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well defined protein environment. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation, and slight differences were found in the Mn-Mn distances determined by XRD, EXAFS and theoretical studies. Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 ångströms using femtosecond X-ray pulses of the SPring-8 ångström compact free-electron laser (SACLA) and hundreds of large, highly isomorphous PSII crystals. Compared with the structure from XRD, the OEC in the X-ray free electron laser structure has Mn-Mn distances that are shorter by 0.1-0.2 ångströms. The valences of each manganese atom were tentatively assigned as Mn1D(III), Mn2C(IV), Mn3B(IV) and Mn4A(III), based on the average Mn-ligand distances and analysis of the Jahn-Teller axis on Mn(III). One of the oxo-bridged oxygens, O5, has significantly longer distances to Mn than do the other oxo-oxygen atoms, suggesting that O5 is a hydroxide ion instead of a normal oxygen dianion and therefore may serve as one of the substrate oxygen atoms. These findings provide a structural basis for the mechanism of oxygen evolution, and we expect that this structure will provide a blueprint for the design of artificial catalysts for water oxidation.

PubMed: 25470056
DOI: 10.1038/nature13991

Experimental method

X-RAY DIFFRACTION (1.95 Å)