5GTH

Native XFEL structure of photosystem II (dark dataset)

Summary for 5GTH

• Entry DOI: 10.2210/pdb5gth/pdb
• Related: 4UB6 5GTI
• Descriptor: Photosystem II protein D1, Photosystem II reaction center protein K, Photosystem II reaction center protein L, ... (41 entities in total)
• Functional Keywords: photosystem ii, photosynthesis, psii, membrane protein
• Biological source: Thermosynechococcus vulcanus; More
• Total number of polymer chains: 39
• Total formula weight: 734581.11

Authors

Suga, M.,Shen, J.R. (deposition date: 2016-08-20, release date: 2017-03-15, Last modification date: 2023-11-08)

Primary citation

Suga, M.,Akita, F.,Sugahara, M.,Kubo, M.,Nakajima, Y.,Nakane, T.,Yamashita, K.,Umena, Y.,Nakabayashi, M.,Yamane, T.,Nakano, T.,Suzuki, M.,Masuda, T.,Inoue, S.,Kimura, T.,Nomura, T.,Yonekura, S.,Yu, L.J.,Sakamoto, T.,Motomura, T.,Chen, J.H.,Kato, Y.,Noguchi, T.,Tono, K.,Joti, Y.,Kameshima, T.,Hatsui, T.,Nango, E.,Tanaka, R.,Naitow, H.,Matsuura, Y.,Yamashita, A.,Yamamoto, M.,Nureki, O.,Yabashi, M.,Ishikawa, T.,Iwata, S.,Shen, J.R.
Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.
Nature, 543:131-135, 2017

PubMed Abstract: Photosystem II (PSII) is a huge membrane-protein complex consisting of 20 different subunits with a total molecular mass of 350 kDa for a monomer. It catalyses light-driven water oxidation at its catalytic centre, the oxygen-evolving complex (OEC). The structure of PSII has been analysed at 1.9 Å resolution by synchrotron radiation X-rays, which revealed that the OEC is a MnCaO cluster organized in an asymmetric, 'distorted-chair' form. This structure was further analysed with femtosecond X-ray free electron lasers (XFEL), providing the 'radiation damage-free' structure. The mechanism of O=O bond formation, however, remains obscure owing to the lack of intermediate-state structures. Here we describe the structural changes in PSII induced by two-flash illumination at room temperature at a resolution of 2.35 Å using time-resolved serial femtosecond crystallography with an XFEL provided by the SPring-8 ångström compact free-electron laser. An isomorphous difference Fourier map between the two-flash and dark-adapted states revealed two areas of apparent changes: around the Q/non-haem iron and the MnCaO cluster. The changes around the Q/non-haem iron region reflected the electron and proton transfers induced by the two-flash illumination. In the region around the OEC, a water molecule located 3.5 Å from the MnCaO cluster disappeared from the map upon two-flash illumination. This reduced the distance between another water molecule and the oxygen atom O4, suggesting that proton transfer also occurred. Importantly, the two-flash-minus-dark isomorphous difference Fourier map showed an apparent positive peak around O5, a unique μ-oxo-bridge located in the quasi-centre of Mn1 and Mn4 (refs 4,5). This suggests the insertion of a new oxygen atom (O6) close to O5, providing an O=O distance of 1.5 Å between these two oxygen atoms. This provides a mechanism for the O=O bond formation consistent with that proposed previously.

PubMed: 28219079
DOI: 10.1038/nature21400

Experimental method

X-RAY DIFFRACTION (2.5 Å)