start-ver=1.4
cd-journal=joma
no-vol=16
cd-vols=
no-issue=1
article-no=
start-page=4175
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2025
dt-pub=20250505
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structure of a photosystem II-FCPII supercomplex from a haptophyte reveals a distinct antenna organization
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Haptophytes are unicellular algae that produce 30 to 50% of biomass in oceans. Among haptophytes, a subset named coccolithophores is characterized by calcified scales. Despite the importance of coccolithophores in global carbon fixation and CaCO3 production, their energy conversion system is still poorly known. Here we report a cryo-electron microscopic structure of photosystem II (PSII)-fucoxanthin chlorophyll c-binding protein (FCPII) supercomplex from Chyrostila roscoffensis, a representative of coccolithophores. This complex has two sets of six dimeric and monomeric FCPIIs, with distinct orientations. Interfaces of both FCPII/FCPII and FCPII/core differ from previously reported. We also determine the sequence of Psb36, a subunit previously found in diatoms and red algae. The principal excitation energy transfer (EET) pathways involve mainly 5 FCPIIs, where one FCPII monomer mediates EET to CP47. Our findings provide a solid structural basis for EET and energy dissipation pathways occurring in coccolithophores.
en-copyright=
kn-copyright=
en-aut-name=La RoccaRomain
en-aut-sei=La Rocca
en-aut-mei=Romain
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=TsaiPi-Cheng
en-aut-sei=Tsai
en-aut-mei=Pi-Cheng
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=NakajimaYoshiki
en-aut-sei=Nakajima
en-aut-mei=Yoshiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University
kn-affil=
affil-num=3
en-affil=Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University
kn-affil=
affil-num=4
en-affil=Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University
kn-affil=
affil-num=5
en-affil=Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University
kn-affil=
affil-num=6
en-affil=Research Institute for Interdisciplinary Science, and Advanced Research Field, Graduate School of Environmental, Life, Natural Science and Technology, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=626
cd-vols=
no-issue=7999
article-no=
start-page=670
end-page=677
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2024
dt-pub=20240131
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Oxygen-evolving photosystem II structures during S1–S2–S3 transitions
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of Si states (i = 0–4) at the Mn4CaO5 cluster1,2,3, during which an extra oxygen (O6) is incorporated at the S3 state to form a possible dioxygen4,5,6,7. 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). YZ, a tyrosine residue that connects the reaction centre P680 and the Mn4CaO5 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 Ca2+ 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.
en-copyright=
kn-copyright=
en-aut-name=LiHongjie
en-aut-sei=Li
en-aut-mei=Hongjie
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=NakajimaYoshiki
en-aut-sei=Nakajima
en-aut-mei=Yoshiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=NangoEriko
en-aut-sei=Nango
en-aut-mei=Eriko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=OwadaShigeki
en-aut-sei=Owada
en-aut-mei=Shigeki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=YamadaDaichi
en-aut-sei=Yamada
en-aut-mei=Daichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=HashimotoKana
en-aut-sei=Hashimoto
en-aut-mei=Kana
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=LuoFangjia
en-aut-sei=Luo
en-aut-mei=Fangjia
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=TanakaRie
en-aut-sei=Tanaka
en-aut-mei=Rie
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=KangJungmin
en-aut-sei=Kang
en-aut-mei=Jungmin
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
en-aut-name=SaitohYasunori
en-aut-sei=Saitoh
en-aut-mei=Yasunori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
ORCID=
en-aut-name=KishiShunpei
en-aut-sei=Kishi
en-aut-mei=Shunpei
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=13
ORCID=
en-aut-name=YuHuaxin
en-aut-sei=Yu
en-aut-mei=Huaxin
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=14
ORCID=
en-aut-name=MatsubaraNaoki
en-aut-sei=Matsubara
en-aut-mei=Naoki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=15
ORCID=
en-aut-name=FujiiHajime
en-aut-sei=Fujii
en-aut-mei=Hajime
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=16
ORCID=
en-aut-name=SugaharaMichihiro
en-aut-sei=Sugahara
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=17
ORCID=
en-aut-name=SuzukiMamoru
en-aut-sei=Suzuki
en-aut-mei=Mamoru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=18
ORCID=
en-aut-name=MasudaTetsuya
en-aut-sei=Masuda
en-aut-mei=Tetsuya
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=19
ORCID=
en-aut-name=KimuraTetsunari
en-aut-sei=Kimura
en-aut-mei=Tetsunari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=20
ORCID=
en-aut-name=ThaoTran Nguyen
en-aut-sei=Thao
en-aut-mei=Tran Nguyen
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=21
ORCID=
en-aut-name=YonekuraShinichiro
en-aut-sei=Yonekura
en-aut-mei=Shinichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=22
ORCID=
en-aut-name=YuLong-Jiang
en-aut-sei=Yu
en-aut-mei=Long-Jiang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=23
ORCID=
en-aut-name=ToshaTakehiko
en-aut-sei=Tosha
en-aut-mei=Takehiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=24
ORCID=
en-aut-name=TonoKensuke
en-aut-sei=Tono
en-aut-mei=Kensuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=25
ORCID=
en-aut-name=JotiYasumasa
en-aut-sei=Joti
en-aut-mei=Yasumasa
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=26
ORCID=
en-aut-name=HatsuiTakaki
en-aut-sei=Hatsui
en-aut-mei=Takaki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=27
ORCID=
en-aut-name=YabashiMakina
en-aut-sei=Yabashi
en-aut-mei=Makina
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=28
ORCID=
en-aut-name=KuboMinoru
en-aut-sei=Kubo
en-aut-mei=Minoru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=29
ORCID=
en-aut-name=IwataSo
en-aut-sei=Iwata
en-aut-mei=So
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=30
ORCID=
en-aut-name=IsobeHiroshi
en-aut-sei=Isobe
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=31
ORCID=
en-aut-name=YamaguchiKizashi
en-aut-sei=Yamaguchi
en-aut-mei=Kizashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=32
ORCID=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=33
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=34
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=3
en-affil=Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
kn-affil=
affil-num=4
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=5
en-affil=Department of Picobiology, Graduate School of Life Science, University of Hyogo
kn-affil=
affil-num=6
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=7
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=8
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=9
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=10
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=11
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=12
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=13
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=14
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=15
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=16
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=17
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=18
en-affil=Institute for Protein Research, Osaka University
kn-affil=
affil-num=19
en-affil=Division of Food and Nutrition, Faculty of Agriculture, Ryukoku University
kn-affil=
affil-num=20
en-affil=Department of Chemistry, Graduate School of Science, Kobe University
kn-affil=
affil-num=21
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=22
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=23
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=24
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=25
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=26
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=27
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=28
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=29
en-affil=Department of Picobiology, Graduate School of Life Science, University of Hyogo
kn-affil=
affil-num=30
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=31
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=32
en-affil=Center for Quantum Information and Quantum Biology, Osaka University
kn-affil=
affil-num=33
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=34
en-affil=Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=471
cd-vols=
no-issue=
article-no=
start-page=214742
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=202211
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Geometric, electronic and spin structures of the CaMn4O5 catalyst for water oxidation in oxygen-evolving photosystem II. Interplay between experiments and theoretical computations
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=The aim of this review is to elucidate geometric structures of the catalytic CaMn4Ox (x = 5, 6) cluster in the Kok cycle for water oxidation in the oxygen evolving complex (OEC) of photosystem II (PSII) based on the high-resolution (HR) X-ray diffraction (XRD) and serial femtosecond crystallography (SFX) experiments using the X-ray free-electron laser (XFEL). Quantum mechanics (QM) and QM/molecular mechanics (MM) computations are performed to elucidate the electronic and spin structures of the CaMn4Ox (x = 5, 6) cluster in five states S-i (i = 0 similar to 4) on the basis of the X-ray spectroscopy, electron paramagnetic resonance (EPR) and related experiments. Interplay between the experiments and theoretical computations has been effective to elucidate the coordination structures of the CaMn4Ox (x = 5, 6) cluster ligated by amino acid residues of the protein matrix of PSII, valence states of the four Mn ions and total spin states by their exchange-couplings, and proton-shifted isomers of the CaMn4Ox (x = 5, 6) cluster. The HR XRD and SFX XFEL experiments have also elucidated the biomolecular systems structure of OEC of PSII and the hydrogen bonding networks consisting of water molecules, chloride anions, etc., for water inlet and proton release pathways in PSII. Large-scale QM/MM computations have been performed for elucidation of the hydrogen bonding distances and angles by adding invisible hydrogen atoms to the HR XRD structure. Full geometry optimizations by the QM and QM/MM methods have been effective for elucidation of the molecular systems structure around the CaMn4Ox (x = 5, 6) cluster in OEC. DLPNO-CCSD(T-0) method has been applied to elucidate relative energies of possible intermediates in each state of the Kok cycle for water oxidation. Implications of these results are discussed in relation to the blueprint for developments of artificial catalysts for water oxidation.
en-copyright=
kn-copyright=
en-aut-name=YamaguchiKizashi
en-aut-sei=Yamaguchi
en-aut-mei=Kizashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=ShojiMitsuo
en-aut-sei=Shoji
en-aut-mei=Mitsuo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=IsobeHiroshi
en-aut-sei=Isobe
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=KawakamiTakashi
en-aut-sei=Kawakami
en-aut-mei=Takashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=MiyagawaKoichi
en-aut-sei=Miyagawa
en-aut-mei=Koichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
affil-num=1
en-affil=Center for Quantum Information and Quantum Biology, Osaka University
kn-affil=
affil-num=2
en-affil=Center of Computational Sciences, Tsukuba University
kn-affil=
affil-num=3
en-affil=Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=4
en-affil=RIKEN Center for Computational Science
kn-affil=
affil-num=5
en-affil=Center of Computational Sciences, Tsukuba University
kn-affil=
affil-num=6
en-affil=Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=7
en-affil=Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=8
en-affil=Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
en-keyword=Water oxidation
kn-keyword=Water oxidation
en-keyword=Oxygen evolution
kn-keyword=Oxygen evolution
en-keyword=Photosystem II
kn-keyword=Photosystem II
en-keyword=HR XRD
kn-keyword=HR XRD
en-keyword=SFX XFEL
kn-keyword=SFX XFEL
en-keyword=QM/MM calculation
kn-keyword=QM/MM calculation
en-keyword=DLPNO CCSD(T-0) computations, Oxyl radical character
kn-keyword=DLPNO CCSD(T-0) computations, Oxyl radical character
END
start-ver=1.4
cd-journal=joma
no-vol=13
cd-vols=
no-issue=1
article-no=
start-page=1764
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=20220401
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Fucoxanthin chlorophyll (Chl) a/c-binding proteins (FCPs) function as light harvesters in diatoms. The structure of a diatom photosystem II-FCPII (PSII-FCPII) supercomplex have been solved by cryo-electron microscopy (cryo-EM) previously; however, the FCPII subunits that constitute the FCPII tetramers and monomers are not identified individually due to their low resolutions. Here, we report a 2.5 angstrom resolution structure of the PSII-FCPII supercomplex using cryo-EM. Two types of tetrameric FCPs, S-tetramer, and M-tetramer, are identified as different types of hetero-tetrameric complexes. In addition, three FCP monomers, m1, m2, and m3, are assigned to different gene products of FCP. The present structure also identifies the positions of most Chls c and diadinoxanthins, which form a complicated pigment network. Excitation-energy transfer from FCPII to PSII is revealed by time-resolved fluorescence spectroscopy. These structural and spectroscopic findings provide insights into an assembly model of FCPII and its excitation-energy transfer and quenching processes. Fucoxanthin chlorophyll a/c-binding proteins (FCPs) harvest light energy in diatoms. The authors analyzed a structure of PSII-FCPII supercomplex at high resolution by cryo-EM, which identified each FCP subunit and pigment network in the supercomplex.
en-copyright=
kn-copyright=
en-aut-name=NagaoRyo
en-aut-sei=Nagao
en-aut-mei=Ryo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=KumazawaMinoru
en-aut-sei=Kumazawa
en-aut-mei=Minoru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=IfukuKentaro
en-aut-sei=Ifuku
en-aut-mei=Kentaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=YokonoMakio
en-aut-sei=Yokono
en-aut-mei=Makio
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=SuzukiTakehiro
en-aut-sei=Suzuki
en-aut-mei=Takehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=DohmaeNaoshi
en-aut-sei=Dohmae
en-aut-mei=Naoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=AkimotoSeiji
en-aut-sei=Akimoto
en-aut-mei=Seiji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=MiyazakiNaoyuki
en-aut-sei=Miyazaki
en-aut-mei=Naoyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=3
en-affil=Graduate School of Biostudies, Kyoto University
kn-affil=
affil-num=4
en-affil=Graduate School of Agriculture, Kyoto University
kn-affil=
affil-num=5
en-affil=Institute of Low Temperature Science, Hokkaido University
kn-affil=
affil-num=6
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=7
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=8
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=9
en-affil=Graduate School of Science, Kobe University
kn-affil=
affil-num=10
en-affil=Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba
kn-affil=
affil-num=11
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=13
cd-vols=
no-issue=1
article-no=
start-page=1679
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2022
dt-pub=20220330
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structure of a tetrameric photosystem I from a glaucophyte alga Cyanophora paradoxa
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosystem I (PSI) is one of the two photosystems functioning in light-energy harvesting, transfer, and electron transfer in photosynthesis. However, the oligomerization state of PSI is variable among photosynthetic organisms. We present a 3.8-angstrom resolution cryo-electron microscopic structure of tetrameric PSI isolated from the glaucophyte alga Cyanophora paradoxa, which reveals differences with PSI from other organisms in subunit composition and organization. The PSI tetramer is organized in a dimer of dimers with a C2 symmetry. Unlike cyanobacterial PSI tetramers, two of the four monomers are rotated around 90 degrees, resulting in a completely different pattern of monomer-monomer interactions. Excitation-energy transfer among chlorophylls differs significantly between Cyanophora and cyanobacterial PSI tetramers. These structural and spectroscopic features reveal characteristic interactions and excitation-energy transfer in the Cyanophora PSI tetramer, suggesting that the Cyanophora PSI could represent a turning point in the evolution of PSI from prokaryotes to eukaryotes.
en-copyright=
kn-copyright=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=NagaoRyo
en-aut-sei=Nagao
en-aut-mei=Ryo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=UenoYoshifumi
en-aut-sei=Ueno
en-aut-mei=Yoshifumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=YokonoMakio
en-aut-sei=Yokono
en-aut-mei=Makio
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=SuzukiTakehiro
en-aut-sei=Suzuki
en-aut-mei=Takehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=Tian-YiJiang
en-aut-sei=Tian-Yi
en-aut-mei=Jiang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=DohmaeNaoshi
en-aut-sei=Dohmae
en-aut-mei=Naoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=AkimotoSeiji
en-aut-sei=Akimoto
en-aut-mei=Seiji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=MiyazakiNaoyuki
en-aut-sei=Miyazaki
en-aut-mei=Naoyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=Jian-RenShen
en-aut-sei=Jian-Ren
en-aut-mei=Shen
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=3
en-affil=Graduate School of Science, Kobe University
kn-affil=
affil-num=4
en-affil=Institute of Low Temperature Science, Hokkaido University
kn-affil=
affil-num=5
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=6
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=7
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=8
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=9
en-affil=Graduate School of Science, Kobe University
kn-affil=
affil-num=10
en-affil=Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba
kn-affil=
affil-num=11
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=4
cd-vols=
no-issue=1
article-no=
start-page=382
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2021
dt-pub=20210322
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.
en-copyright=
kn-copyright=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=MiyazakiNaoyuki
en-aut-sei=Miyazaki
en-aut-mei=Naoyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=HamaguchiTasuku
en-aut-sei=Hamaguchi
en-aut-mei=Tasuku
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=NakajimaYoshiki
en-aut-sei=Nakajima
en-aut-mei=Yoshiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=YonekuraKoji
en-aut-sei=Yonekura
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba
kn-affil=
affil-num=3
en-affil=Biostructural Mechanism Laboratory, RIKEN Spring-8 Center
kn-affil=
affil-num=4
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=5
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=6
en-affil=Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
kn-affil=
affil-num=7
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=3
cd-vols=
no-issue=1
article-no=
start-page=232
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200511
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structure of a cyanobacterial photosystem I surrounded by octadecameric IsiA antenna proteins
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Iron-stress induced protein A (IsiA) is a chlorophyll-binding membrane-spanning protein in photosynthetic prokaryote cyanobacteria, and is associated with photosystem I (PSI) trimer cores, but its structural and functional significance in light harvesting remains unclear. Here we report a 2.7-angstrom resolution cryo-electron microscopic structure of a supercomplex between PSI core trimer and IsiA from a thermophilic cyanobacterium Thermosynechococcus vulcanus. The structure showed that 18 IsiA subunits form a closed ring surrounding a PSI trimer core. Detailed arrangement of pigments within the supercomplex, as well as molecular interactions between PSI and IsiA and among IsiAs, were resolved. Time-resolved fluorescence spectra of the PSI-IsiA supercomplex showed clear excitation-energy transfer from IsiA to PSI, strongly indicating that IsiA functions as an energy donor, but not an energy quencher, in the supercomplex. These structural and spectroscopic findings provide important insights into the excitation-energy-transfer and subunit assembly mechanisms in the PSI-IsiA supercomplex. Akita et al. present the latest approach to solve IsiA-PSI supercomplex molecular structure with increased resolution using cryo-EM and time-resolved fluorescence studies. With 2.7 angstrom resolution, they reveal molecular interactions between PSI and IsiA subunits and that IsiA functions as an energy donor in the supercomplex.
en-copyright=
kn-copyright=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=NagaoRyo
en-aut-sei=Nagao
en-aut-mei=Ryo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=NakajimaYoshiki
en-aut-sei=Nakajima
en-aut-mei=Yoshiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=YokonoMakio
en-aut-sei=Yokono
en-aut-mei=Makio
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=UenoYoshifumi
en-aut-sei=Ueno
en-aut-mei=Yoshifumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=SuzukiTakehiro
en-aut-sei=Suzuki
en-aut-mei=Takehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=DohmaeNaoshi
en-aut-sei=Dohmae
en-aut-mei=Naoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=AkimotoSeiji
en-aut-sei=Akimoto
en-aut-mei=Seiji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=MiyazakiNaoyuki
en-aut-sei=Miyazaki
en-aut-mei=Naoyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
affil-num=1
en-affil=Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=3
en-affil=Research Institute for Interdisciplinary Science, Okayama University
kn-affil=
affil-num=4
en-affil=Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=5
en-affil=Nippon Flour Mills Co., Ltd., Innovation Center
kn-affil=
affil-num=6
en-affil=Graduate School of Science, Kobe University
kn-affil=
affil-num=7
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=8
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=9
en-affil= Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=10
en-affil=Graduate School of Science, Kobe University
kn-affil=
affil-num=11
en-affil=Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba
kn-affil=
en-keyword=Cryoelectron microscopy
kn-keyword=Cryoelectron microscopy
en-keyword=Photosystem I
kn-keyword=Photosystem I
END
start-ver=1.4
cd-journal=joma
no-vol=11
cd-vols=
no-issue=1
article-no=
start-page=
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200518
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c-binding proteins (FCPs) present in diatoms, a group of organisms having important contribution to the global carbon cycle. Here, we report a 2.40-angstrom resolution structure of the diatom photosystem I (PSI)-FCPI supercomplex by cryo-electron microscopy. The supercomplex is composed of 16 different FCPI subunits surrounding a monomeric PSI core. Each FCPI subunit showed different protein structures with different pigment contents and binding sites, and they form a complicated pigment-protein network together with the PSI core to harvest and transfer the light energy efficiently. In addition, two unique, previously unidentified subunits were found in the PSI core. The structure provides numerous insights into not only the light-harvesting strategy in diatom PSI-FCPI but also evolutionary dynamics of light harvesters among oxyphototrophs. One of the major photosynthetic light-harvesting complexes (LHCs) are fucoxanthin chlorophyll a/c-binding proteins (FCPs), which are present in diatoms, a major group of algae. Here, the authors present the cryo-EM structure of the photosystem I-FCP (PSI-FCPI) supercomplex isolated from the marine centric diatom Chaetoceros gracilis that contains 16 FCPI subunits surrounding the PSI core and discuss possible excitation energy transfer pathways.
en-copyright=
kn-copyright=
en-aut-name=NagaoRyo
en-aut-sei=Nagao
en-aut-mei=Ryo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=IfukuKentaro
en-aut-sei=Ifuku
en-aut-mei=Kentaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=SuzukiTakehiro
en-aut-sei=Suzuki
en-aut-mei=Takehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=KumazawaMinoru
en-aut-sei=Kumazawa
en-aut-mei=Minoru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=UchiyamaIkuo
en-aut-sei=Uchiyama
en-aut-mei=Ikuo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=KashinoYasuhiro
en-aut-sei=Kashino
en-aut-mei=Yasuhiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=DohmaeNaoshi
en-aut-sei=Dohmae
en-aut-mei=Naoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=AkimotoSeiji
en-aut-sei=Akimoto
en-aut-mei=Seiji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=MiyazakiNaoyuki
en-aut-sei=Miyazaki
en-aut-mei=Naoyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=3
en-affil=Graduate School of Biostudies, Kyoto University
kn-affil=
affil-num=4
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=5
en-affil=Faculty of Agriculture, Kyoto University
kn-affil=
affil-num=6
en-affil=National Institute for Basic Biology, National Institutes of Natural Sciences
kn-affil=
affil-num=7
en-affil=Graduate School of Life Science, University of Hyogo
kn-affil=
affil-num=8
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=9
en-affil=Graduate School of Science,Kobe University
kn-affil=
affil-num=10
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=11
en-affil=Institute for Protein Research, Osaka University
kn-affil=
affil-num=12
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=11
cd-vols=
no-issue=1
article-no=
start-page=238
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200113
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Structural basis for the adaptation and function of chlorophyll f in photosystem I
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f.
en-copyright=
kn-copyright=
en-aut-name=KatoKoji
en-aut-sei=Kato
en-aut-mei=Koji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=ShinodaToshiyuki
en-aut-sei=Shinoda
en-aut-mei=Toshiyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=NagaoRyo
en-aut-sei=Nagao
en-aut-mei=Ryo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=AkimotoSeiji
en-aut-sei=Akimoto
en-aut-mei=Seiji
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=SuzukiTakehiro
en-aut-sei=Suzuki
en-aut-mei=Takehiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=DohmaeNaoshi
en-aut-sei=Dohmae
en-aut-mei=Naoshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=ChenMin
en-aut-sei=Chen
en-aut-mei=Min
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=AllakhverdievSuleyman I.
en-aut-sei=Allakhverdiev
en-aut-mei=Suleyman I.
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=MiyazakiNaoyuki
en-aut-sei=Miyazaki
en-aut-mei=Naoyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
en-aut-name=TomoTatsuya
en-aut-sei=Tomo
en-aut-mei=Tatsuya
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Faculty of Science, Tokyo University of Science
kn-affil=
affil-num=3
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=4
en-affil=Graduate School of Science, Kobe University
kn-affil=
affil-num=5
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=6
en-affil=Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science
kn-affil=
affil-num=7
en-affil=School of Life and Environmental Sciences, University of Sydney
kn-affil=
affil-num=8
en-affil=K.A. Timiryazev Institute of Plant Physiology RAS
kn-affil=
affil-num=9
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=10
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=11
en-affil=Institute for Protein Research, Laboratory of Protein Synthesis and Expression, Osaka University
kn-affil=
affil-num=12
en-affil=Faculty of Science, Tokyo University of Science
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=1864
cd-vols=
no-issue=2
article-no=
start-page=129466
end-page=
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2020
dt-pub=20200229
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Time-resolved studies of metalloproteins using X-ray free electron laser radiation at SACLA
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract=Background: The invention of the X-ray free-electron laser (XFEL) has provided unprecedented new opportunities for structural biology. The advantage of XFEL is an intense pulse of X-rays and a very short pulse duration (<10 fs) promising a damage-free and time-resolved crystallography approach.
Scope of review: Recent time-resolved crystallographic analyses in XFEL facility SACLA are reviewed. Specifically, metalloproteins involved in the essential reactions of bioenergy conversion including photosystem II, cytochrome c oxidase and nitric oxide reductase are described.
Major conclusions: XFEL with pump-probe techniques successfully visualized the process of the reaction and the dynamics of a protein. Since the active center of metalloproteins is very sensitive to the X-ray radiation, damage-free structures obtained by XFEL are essential to draw mechanistic conclusions. Methods and tools for sample delivery and reaction initiation are key for successful measurement of the time-resolved data.
General significance: XFEL is at the center of approaches to gain insight into complex mechanism of structural dynamics and the reactions catalyzed by biological macromolecules. Further development has been carried out to expand the application of time-resolved X-ray crystallography. This article is part of a Special Issue entitled Novel measurement techniques for visualizing 'live' protein molecules.
en-copyright=
kn-copyright=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=ShimadaAtsuhiro
en-aut-sei=Shimada
en-aut-mei=Atsuhiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=ToshaTakehiko
en-aut-sei=Tosha
en-aut-mei=Takehiko
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=SugimotoHiroshi
en-aut-sei=Sugimoto
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Graduate School of Applied Biological Sciences and Faculty of Applied Biological Sciences, Gifu University
kn-affil=
affil-num=3
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=4
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=5
en-affil=Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center
kn-affil=
affil-num=6
en-affil=Synchrotron Radiation Life Science Instrumentation Team, RIKEN SPring-8 Center
kn-affil=
en-keyword=Heme
kn-keyword=Heme
en-keyword=Metalloproteins
kn-keyword=Metalloproteins
en-keyword=Proton pump
kn-keyword=Proton pump
en-keyword=Radiation damage
kn-keyword=Radiation damage
en-keyword=Serial femtosecond crystallography
kn-keyword=Serial femtosecond crystallography
en-keyword=X-ray free-electron laser
kn-keyword=X-ray free-electron laser
END
start-ver=1.4
cd-journal=joma
no-vol=366
cd-vols=
no-issue=6463
article-no=
start-page=334
end-page=338
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2019
dt-pub=20191018
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=An oxyl/oxo mechanism for dioxygen bond formation in PSII revealed by X-ray free electron lasers
en-subtitle=
kn-subtitle=
en-abstract=
kn-abstract= Photosynthetic water oxidation is catalyzed by the Mn4CaO5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S0 to S4). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S1, S2, and S3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S2, but flipping of D1 Glu189 upon transition to S3 leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn4CaO6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.
en-copyright=
kn-copyright=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=YamashitaKeitaro
en-aut-sei=Yamashita
en-aut-mei=Keitaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=NakajimaYoshiki
en-aut-sei=Nakajima
en-aut-mei=Yoshiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=UenoGo
en-aut-sei=Ueno
en-aut-mei=Go
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=LiHongjie
en-aut-sei=Li
en-aut-mei=Hongjie
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=YamaneTakahiro
en-aut-sei=Yamane
en-aut-mei=Takahiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=HirataKunio
en-aut-sei=Hirata
en-aut-mei=Kunio
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=UmenaYasufumi
en-aut-sei=Umena
en-aut-mei=Yasufumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=YonekuraShinichiro
en-aut-sei=Yonekura
en-aut-mei=Shinichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=YuLong-Jiang
en-aut-sei=Yu
en-aut-mei=Long-Jiang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
en-aut-name=MurakamiHironori
en-aut-sei=Murakami
en-aut-mei=Hironori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
ORCID=
en-aut-name=NomuraTakashi
en-aut-sei=Nomura
en-aut-mei=Takashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=13
ORCID=
en-aut-name=KimuraTetsunari
en-aut-sei=Kimura
en-aut-mei=Tetsunari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=14
ORCID=
en-aut-name=KuboMinoru
en-aut-sei=Kubo
en-aut-mei=Minoru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=15
ORCID=
en-aut-name=BabaSeiki
en-aut-sei=Baba
en-aut-mei=Seiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=16
ORCID=
en-aut-name=KumasakaTakashi
en-aut-sei=Kumasaka
en-aut-mei=Takashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=17
ORCID=
en-aut-name=TonoKensuke
en-aut-sei=Tono
en-aut-mei=Kensuke
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=18
ORCID=
en-aut-name=YabashiMakina
en-aut-sei=Yabashi
en-aut-mei=Makina
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=19
ORCID=
en-aut-name=IsobeHiroshi
en-aut-sei=Isobe
en-aut-mei=Hiroshi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=20
ORCID=
en-aut-name=YamaguchiKizashi
en-aut-sei=Yamaguchi
en-aut-mei=Kizashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=21
ORCID=
en-aut-name=YamamotoMasaki
en-aut-sei=Yamamoto
en-aut-mei=Masaki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=22
ORCID=
en-aut-name=AgoHideo
en-aut-sei=Ago
en-aut-mei=Hideo
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=23
ORCID=
en-aut-name=ShenJian-Ren
en-aut-sei=Shen
en-aut-mei=Jian-Ren
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=24
ORCID=
affil-num=1
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=2
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=3
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=4
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=5
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=6
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=7
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=8
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=9
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=10
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=11
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=12
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=13
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=14
en-affil=Department of Chemistry, Graduate School of Science, Kobe University
kn-affil=
affil-num=15
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=16
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=17
en-affil=Japan Synchrotron Radiation Research Institute
kn-affil=
affil-num=18
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=19
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=20
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=21
en-affil=The Institute for Scientific and Industrial Research, Osaka University
kn-affil=
affil-num=22
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=23
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=24
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=543
cd-vols=
no-issue=7643
article-no=
start-page=131
end-page=135
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2017
dt-pub=201703
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL
en-subtitle=
kn-subtitle=
en-abstract=
kn-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 Mn4CaO5 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 QB/non-haem iron and the Mn4CaO5 cluster. The changes around the QB/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 Mn4CaO5 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 μ4-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
en-copyright=
kn-copyright=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=AkitaFusamichi
en-aut-sei=Akita
en-aut-mei=Fusamichi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=2
ORCID=
en-aut-name=SugaharaMichihiro
en-aut-sei=Sugahara
en-aut-mei=Michihiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=3
ORCID=
en-aut-name=KuboMinoru
en-aut-sei=Kubo
en-aut-mei=Minoru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=4
ORCID=
en-aut-name=NakajimaYoshiki
en-aut-sei=Nakajima
en-aut-mei=Yoshiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=5
ORCID=
en-aut-name=NakaneTakanori
en-aut-sei=Nakane
en-aut-mei=Takanori
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=6
ORCID=
en-aut-name=YamashitaKeitaro
en-aut-sei=Yamashita
en-aut-mei=Keitaro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=7
ORCID=
en-aut-name=UmenaYasufumi
en-aut-sei=Umena
en-aut-mei=Yasufumi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=8
ORCID=
en-aut-name=NakabayashiMakoto
en-aut-sei=Nakabayashi
en-aut-mei=Makoto
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=9
ORCID=
en-aut-name=YamaneTakahiro
en-aut-sei=Yamane
en-aut-mei=Takahiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=10
ORCID=
en-aut-name=NakanoTakamitsu
en-aut-sei=Nakano
en-aut-mei=Takamitsu
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=11
ORCID=
en-aut-name=SuzukiMamoru
en-aut-sei=Suzuki
en-aut-mei=Mamoru
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=12
ORCID=
en-aut-name=MasudaTetsuya
en-aut-sei=Masuda
en-aut-mei=Tetsuya
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=13
ORCID=
en-aut-name=InoueShigeyuki
en-aut-sei=Inoue
en-aut-mei=Shigeyuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=14
ORCID=
en-aut-name=KimuraTetsunari
en-aut-sei=Kimura
en-aut-mei=Tetsunari
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=15
ORCID=
en-aut-name=NomuraTakashi
en-aut-sei=Nomura
en-aut-mei=Takashi
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=16
ORCID=
en-aut-name=YonekuraShinichiro
en-aut-sei=Yonekura
en-aut-mei=Shinichiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=17
ORCID=
en-aut-name=YuLong-Jiang
en-aut-sei=Yu
en-aut-mei=Long-Jiang
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=18
ORCID=
en-aut-name=SakamotoTomohiro
en-aut-sei=Sakamoto
en-aut-mei=Tomohiro
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=19
ORCID=
en-aut-name=MotomuraTaiki
en-aut-sei=Motomura
en-aut-mei=Taiki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=20
ORCID=
en-aut-name=ChenJing-Hua
en-aut-sei=Chen
en-aut-mei=Jing-Hua
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=21
ORCID=
en-aut-name=KatoYuki
en-aut-sei=Kato
en-aut-mei=Yuki
kn-aut-name=
kn-aut-sei=
kn-aut-mei=
aut-affil-num=22
ORCID=
en-aut-name=NoguchiTakumi
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affil-num=2
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=3
en-affil=RIKEN SPring-8 Center
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affil-num=4
en-affil=Japan Science and Technology Agency, PRESTO
kn-affil=
affil-num=5
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=6
en-affil=Department of Biological Sciences, Graduate School of Science, The University of Tokyo
kn-affil=
affil-num=7
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=8
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=9
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=10
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=11
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=12
en-affil=Institute for Protein Research, Osaka University
kn-affil=
affil-num=13
en-affil=Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University
kn-affil=
affil-num=14
en-affil=Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo
kn-affil=
affil-num=15
en-affil=Department of Chemistry, Graduate School of Science, Kobe University
kn-affil=
affil-num=16
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=17
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
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affil-num=18
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
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en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=20
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=21
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
affil-num=22
en-affil=Division of Material Science, Graduate School of Science, Nagoya University
kn-affil=
affil-num=23
en-affil=Division of Material Science, Graduate School of Science, Nagoya University
kn-affil=
affil-num=24
en-affil=Japan Synchrotron Radiation Research Institute
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affil-num=25
en-affil=Japan Synchrotron Radiation Research Institute
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affil-num=32
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=33
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=34
en-affil=Department of Biological Sciences, Graduate School of Science, The University of Tokyo
kn-affil=
affil-num=35
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=36
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=37
en-affil=RIKEN SPring-8 Center
kn-affil=
affil-num=38
en-affil=Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University
kn-affil=
END
start-ver=1.4
cd-journal=joma
no-vol=517
cd-vols=
no-issue=
article-no=
start-page=99
end-page=103
dt-received=
dt-revised=
dt-accepted=
dt-pub-year=2015
dt-pub=20150101
dt-online=
en-article=
kn-article=
en-subject=
kn-subject=
en-title=
kn-title=Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses
en-subtitle=
kn-subtitle=
en-abstract=
kn-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 which 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 (Å) resolution, which revealed that the OEC is a Mn4CaO5-cluster coordinated by a well-defined protein environment1. However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation2, and slight differences were found in the Mn–Mn distances between the results of XRD1, EXAFS3–7 and theoretical studies8–14. Here we report a ‘radiation-damage-free’ structure of PSII from Thermosynechococcus vulcanus in the S1 state at a resolution of 1.95 Å using femtosecond X-ray pulses of the SPring-8 ångström compact free-electron laser (SACLA) and a huge number 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 Å. 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 Mn–O distances in contrast to the other oxo-oxygen atoms, suggesting that it 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 design of artificial catalysts for water oxidation.
en-copyright=
kn-copyright=
en-aut-name=SugaMichihiro
en-aut-sei=Suga
en-aut-mei=Michihiro
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kn-aut-mei=
aut-affil-num=1
ORCID=
en-aut-name=AkitaFusamichi
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en-aut-name=NakajimaYoshiki
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en-aut-name=YamashitaKeitaro
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affil-num=3
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kn-affil=Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University
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kn-affil=Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University
END