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286 results on '"Yamashita, Keitaro"'

1. Structural mechanism of bridge RNA-guided recombination.

Author

Hiraizumi, Masahiro, Perry, Nicholas, Durrant, Matthew, Soma, Teppei, Nagahata, Naoto, Okazaki, Sae, Athukoralage, Januka, Isayama, Yukari, Pai, James, Pawluk, April, Konermann, Silvana, Yamashita, Keitaro, Hsu, Patrick, and Nishimasu, Hiroshi

Subjects
Recombinases, DNA, DNA Transposable Elements, RNA, Untranslated, Cryoelectron Microscopy, Recombination, Genetic, Catalytic Domain, Nucleic Acid Conformation, Substrate Specificity, Models, Molecular, Protein Multimerization
Abstract

Insertion sequence (IS) elements are the simplest autonomous transposable elements found in prokaryotic genomes1. We recently discovered that IS110 family elements encode a recombinase and a non-coding bridge RNA (bRNA) that confers modular specificity for target DNA and donor DNA through two programmable loops2. Here we report the cryo-electron microscopy structures of the IS110 recombinase in complex with its bRNA, target DNA and donor DNA in three different stages of the recombination reaction cycle. The IS110 synaptic complex comprises two recombinase dimers, one of which houses the target-binding loop of the bRNA and binds to target DNA, whereas the other coordinates the bRNA donor-binding loop and donor DNA. We uncovered the formation of a composite RuvC-Tnp active site that spans the two dimers, positioning the catalytic serine residues adjacent to the recombination sites in both target and donor DNA. A comparison of the three structures revealed that (1) the top strands of target and donor DNA are cleaved at the composite active sites to form covalent 5-phosphoserine intermediates, (2) the cleaved DNA strands are exchanged and religated to create a Holliday junction intermediate, and (3) this intermediate is subsequently resolved by cleavage of the bottom strands. Overall, this study reveals the mechanism by which a bispecific RNA confers target and donor DNA specificity to IS110 recombinases for programmable DNA recombination.

Published
2024

3. Graph Signal Sampling Under Smoothness Priors: A Difference-of-Convex Approach

Author

Ono, Shunsuke, Naganuma, Kazuki, and Yamashita, Keitaro

Subjects
Electrical Engineering and Systems Science - Signal Processing
Abstract

This paper proposes a method for properly sampling graph signals under smoothness priors. Unlike many existing approaches that assume bandlimited graph signals, our method designs a sampling operator for graph signals that are not necessarily bandlimited based on the generalized sampling theory. First, we formulate the sampling operator design under smoothness priors as a feasibility problem. Then, we transform this problem into a Difference-of-Convex (DC) problem by relaxing a certain invertibility constraint in the original problem using the nuclear norm. Furthermore, we develop an efficient algorithm to solve this DC problem based on the proximal linearized difference-of-convex algorithm and guarantee its convergence to a critical point of the problem. Finally, we demonstrate the effectiveness of our method for several graph signal models through sampling-and-reconstruction experiments., Comment: Submitted to IEEE Signal Processing Letters. The source code is available at https://drive.google.com/file/d/1Ulc9ef2Pl9ucJT0U5lhGoaZCCfldXCQp/view?usp=sharing

Published
2023

6. Structural basis for ion selectivity in potassium-selective channelrhodopsins

Author

Tajima, Seiya, Kim, Yoon Seok, Fukuda, Masahiro, Jo, YoungJu, Wang, Peter Y., Paggi, Joseph M., Inoue, Masatoshi, Byrne, Eamon F.X., Kishi, Koichiro E., Nakamura, Seiwa, Ramakrishnan, Charu, Takaramoto, Shunki, Nagata, Takashi, Konno, Masae, Sugiura, Masahiro, Katayama, Kota, Matsui, Toshiki E., Yamashita, Keitaro, Kim, Suhyang, Ikeda, Hisako, Kim, Jaeah, Kandori, Hideki, Dror, Ron O., Inoue, Keiichi, Deisseroth, Karl, and Kato, Hideaki E.

Published
2023
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10. Short-lived intermediate in N₂O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography

Author

Nomura, Takashi, Kimura, Tetsunari, Kanematsu, Yusuke, Yamada, Daichi, Yamashita, Keitaro, Hirata, Kunio, Ueno, Go, Murakami, Hironori, Hisano, Tamao, Yamagiwa, Raika, Takeda, Hanae, Gopalasingam, Chai, Kousaka, Ryota, Yanagisawa, Sachiko, Shoji, Osami, Kumasaka, Takashi, Yamamoto, Masaki, Takano, Yu, Sugimoto, Hiroshi, Tosha, Takehiko, Kubo, Minoru, and Shiro, Yoshitsugu

Published
2021

12. Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine

Author

Kishi, Koichiro E., Kim, Yoon Seok, Fukuda, Masahiro, Inoue, Masatoshi, Kusakizako, Tsukasa, Wang, Peter Y., Ramakrishnan, Charu, Byrne, Eamon F.X., Thadhani, Elina, Paggi, Joseph M., Matsui, Toshiki E., Yamashita, Keitaro, Nagata, Takashi, Konno, Masae, Quirin, Sean, Lo, Maisie, Benster, Tyler, Uemura, Tomoko, Liu, Kehong, Shibata, Mikihiro, Nomura, Norimichi, Iwata, So, Nureki, Osamu, Dror, Ron O., Inoue, Keiichi, Deisseroth, Karl, and Kato, Hideaki E.

Published
2022
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20. Cryo-EM structure of the human MT1–Gi signaling complex

Author

Okamoto, Hiroyuki H., Miyauchi, Hirotake, Inoue, Asuka, Raimondi, Francesco, Tsujimoto, Hirokazu, Kusakizako, Tsukasa, Shihoya, Wataru, Yamashita, Keitaro, Suno, Ryoji, Nomura, Norimichi, Kobayashi, Takuya, Iwata, So, Nishizawa, Tomohiro, and Nureki, Osamu

Published
2021
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22. Structure determination by cryoEM at 100 keV

Author

McMullan, Greg, primary, Naydenova, Katerina, additional, Mihaylov, Daniel, additional, Yamashita, Keitaro, additional, Peet, Mathew J., additional, Wilson, Hugh, additional, Dickerson, Joshua L., additional, Chen, Shaoxia, additional, Cannone, Giuseppe, additional, Lee, Yang, additional, Hutchings, Katherine A., additional, Gittins, Olivia, additional, Sobhy, Mohamed A., additional, Wells, Torquil, additional, El-Gomati, Mohamed M., additional, Dalby, Jason, additional, Meffert, Matthias, additional, Schulze-Briese, Clemens, additional, Henderson, Richard, additional, and Russo, Christopher J., additional

Published
2023
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23. Crystal structure of heliorhodopsin

Author

Shihoya, Wataru, Inoue, Keiichi, Singh, Manish, Konno, Masae, Hososhima, Shoko, Yamashita, Keitaro, and Ikeda, Kento

Subjects
Crystals -- Structure, Rhodopsin -- Structure, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Heliorhodopsins (HeRs) are a family of rhodopsins that was recently discovered using functional metagenomics.sup.1. They are widely present in bacteria, archaea, algae and algal viruses.sup.2,3. Although HeRs have seven predicted transmembrane helices and an all-trans retinal chromophore as in the type-1 (microbial) rhodopsin, they display less than 15% sequence identity with type-1 and type-2 (animal) rhodopsins. HeRs also exhibit the reverse orientation in the membrane compared with the other rhodopsins. Owing to the lack of structural information, little is known about the overall fold and the photoactivation mechanism of HeRs. Here we present the 2.4-Å-resolution structure of HeR from an uncultured Thermoplasmatales archaeon SG8-52-1 (GenBank sequence ID LSSD01000000). Structural and biophysical analyses reveal the similarities and differences between HeRs and type-1 microbial rhodopsins. The overall fold of HeR is similar to that of bacteriorhodopsin. A linear hydrophobic pocket in HeR accommodates a retinal configuration and isomerization as in the type-1 rhodopsin, although most of the residues constituting the pocket are divergent. Hydrophobic residues fill the space in the extracellular half of HeR, preventing the permeation of protons and ions. The structure reveals an unexpected lateral fenestration above the [beta]-ionone ring of the retinal chromophore, which has a critical role in capturing retinal from environment sources. Our study increases the understanding of the functions of HeRs, and the structural similarity and diversity among the microbial rhodopsins. A crystal structure of Thermoplasmatales archaeon heliorhodopsin at 2.4 Å resolution shows that it adopts a similar fold to that of type I rhodopsin--despite the low sequence identity--but there are also several marked differences that provide insights into heliorhodopsin function., Author(s): Wataru Shihoya [sup.1] , Keiichi Inoue [sup.2] [sup.3] [sup.4] [sup.5] , Manish Singh [sup.2] , Masae Konno [sup.2] , Shoko Hososhima [sup.2] , Keitaro Yamashita [sup.1] [sup.6] , Kento [...]

Published
2019
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24. Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA

Author

Suno, Ryoji, Kimura, Kanako Terakado, Nakane, Takanori, Yamashita, Keitaro, Wang, Junmei, Fujiwara, Takaaki, Yamanaka, Yasuaki, Im, Dohyun, Horita, Shoichiro, Tsujimoto, Hirokazu, Tawaramoto, Maki S., Hirokawa, Takatsugu, Nango, Eriko, Tono, Kensuke, Kameshima, Takashi, Hatsui, Takaki, Joti, Yasumasa, Yabashi, Makina, Shimamoto, Keiko, Yamamoto, Masaki, Rosenbaum, Daniel M., Iwata, So, Shimamura, Tatsuro, and Kobayashi, Takuya

Published
2018
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25. Isoprenoid-chained lipid EROCOC17+4: a new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography

Author

Ihara, Kentaro, Hato, Masakatsu, Nakane, Takanori, Yamashita, Keitaro, Kimura-Someya, Tomomi, Hosaka, Toshiaki, Ishizuka-Katsura, Yoshiko, Tanaka, Rie, Tanaka, Tomoyuki, Sugahara, Michihiro, Hirata, Kunio, Yamamoto, Masaki, Nureki, Osamu, Tono, Kensuke, Nango, Eriko, Iwata, So, and Shirouzu, Mikako

Published
2020
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26. Crystal structure of Drosophila Piwi

Author

Yamaguchi, Sonomi, Oe, Akira, Nishida, Kazumichi M., Yamashita, Keitaro, Kajiya, Asako, Hirano, Seiichi, Matsumoto, Naoki, Dohmae, Naoshi, Ishitani, Ryuichiro, Saito, Kuniaki, Siomi, Haruhiko, Nishimasu, Hiroshi, Siomi, Mikiko C., and Nureki, Osamu

Published
2020
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27. Crystal structure of the natural anion-conducting channelrhodopsin GtACR1

Author

Kim, Yoon Seok, Kato, Hideaki E., Yamashita, Keitaro, Ito, Shota, Inoue, Keiichi, Ramakrishnan, Charu, and Fenno, Lief E.

Subjects
Crystal structure -- Research, Rhodopsin -- Structure -- Chemical properties, Neurons, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The naturally occurring channelrhodopsin variant anion channelrhodopsin-1 (ACR1), discovered in the cryptophyte algae Guillardia theta, exhibits large light-gated anion conductance and high anion selectivity when expressed in heterologous settings, properties that support its use as an optogenetic tool to inhibit neuronal firing with light. However, molecular insight into ACR1 is lacking owing to the absence of structural information underlying light-gated anion conductance. Here we present the crystal structure of G. theta ACR1 at 2.9 Å resolution. The structure reveals unusual architectural features that span the extracellular domain, retinal-binding pocket, Schiff-base region, and anion-conduction pathway. Together with electrophysiological and spectroscopic analyses, these findings reveal the fundamental molecular basis of naturally occurring light-gated anion conductance, and provide a framework for designing the next generation of optogenetic tools.The crystal structure of anion channelrhodopsin-1 (ACR1) from the algae Guillardia theta provides insights into the basis of anion conductance., Author(s): Yoon Seok Kim [sup.1] , Hideaki E. Kato [sup.2] [sup.3] , Keitaro Yamashita [sup.4] , Shota Ito [sup.5] , Keiichi Inoue [sup.3] [sup.5] [sup.6] , Charu Ramakrishnan [sup.1] , [...]

Published
2018
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32. The CCP4 suite: integrative software for macromolecular crystallography

Author

Agirre, Jon, Atanasova, Mihaela, Bagdonas, Haroldas, Ballard, Charles B., Basle, Arnaud, Beilsten-Edmands, James, Borges, Rafael J., Brown, David G., Burgos-Marmol, J. Javier, Berrisford, John M., Bond, Paul S., Caballero, Iracema, Catapano, Lucrezia, Chojnowski, Grzegorz, Cook, Atlanta G., Cowtan, Kevin D., Croll, Tristan I., Debreczeni, Judit E., Devenish, Nicholas E., Dodson, Eleanor J., Drevon, Tarik R., Emsley, Paul, Evans, Gwyndaf, Evans, Phil R., Fando, Maria, Foadi, James, Fuentes-Montero, Luis, Garman, Elspeth F., Gerstel, Markus, Gildea, Richard J., Hatti, Kaushik, Hekkelman, Maarten L., Heuser, Philipp, Hoh, Soon Wen, Hough, Michael A., Jenkins, Huw T., Jimenez, Elisabet, Joosten, Robbie P., Keegan, Ronan M., Keep, Nicholas, Krissinel, Eugene B., Kolenko, Petr, Kovalevskiy, Oleg, Lamzin, Victor S., Lawson, David M., Lebedev, Andrey A., Leslie, Andrew G. W., Lohkamp, Bernhard, Long, Fei, Maly, Martin, McCoy, Airlie J., McNicholas, Stuart J., Medina, Ana, Millan, Claudia, Murray, James W., Murshudov, Garib N., Nicholls, Robert A., Noble, Martin E. M., Oeffner, Robert, Pannu, Navraj S., Parkhurst, James M., Pearce, Nicholas, Pereira, Joana, Perrakis, Anastassis, Powell, Harold R., Read, Randy J., Rigden, Daniel J., Rochira, William, Sammito, Massimo, Rodriguez, Filomeno Sanchez, Sheldrick, George M., Shelley, Kathryn L., Simkovic, Felix, Simpkin, Adam J., Skubak, Pavol, Sobolev, Egor, Steiner, Roberto A., Stevenson, Kyle, Tews, Ivo, Thomas, Jens M. H., Thorn, Andrea, Trivino Valls, Josep, Uski, Ville, Uson, Isabel, Vagin, Alexei, Velankar, Sameer, Vollmar, Melanie, Walden, Helen, Waterman, David, Wilson, Keith S., Winn, Martyn D., Winter, Graeme, Wojdyr, Marcin, Yamashita, Keitaro, Agirre, Jon, Atanasova, Mihaela, Bagdonas, Haroldas, Ballard, Charles B., Basle, Arnaud, Beilsten-Edmands, James, Borges, Rafael J., Brown, David G., Burgos-Marmol, J. Javier, Berrisford, John M., Bond, Paul S., Caballero, Iracema, Catapano, Lucrezia, Chojnowski, Grzegorz, Cook, Atlanta G., Cowtan, Kevin D., Croll, Tristan I., Debreczeni, Judit E., Devenish, Nicholas E., Dodson, Eleanor J., Drevon, Tarik R., Emsley, Paul, Evans, Gwyndaf, Evans, Phil R., Fando, Maria, Foadi, James, Fuentes-Montero, Luis, Garman, Elspeth F., Gerstel, Markus, Gildea, Richard J., Hatti, Kaushik, Hekkelman, Maarten L., Heuser, Philipp, Hoh, Soon Wen, Hough, Michael A., Jenkins, Huw T., Jimenez, Elisabet, Joosten, Robbie P., Keegan, Ronan M., Keep, Nicholas, Krissinel, Eugene B., Kolenko, Petr, Kovalevskiy, Oleg, Lamzin, Victor S., Lawson, David M., Lebedev, Andrey A., Leslie, Andrew G. W., Lohkamp, Bernhard, Long, Fei, Maly, Martin, McCoy, Airlie J., McNicholas, Stuart J., Medina, Ana, Millan, Claudia, Murray, James W., Murshudov, Garib N., Nicholls, Robert A., Noble, Martin E. M., Oeffner, Robert, Pannu, Navraj S., Parkhurst, James M., Pearce, Nicholas, Pereira, Joana, Perrakis, Anastassis, Powell, Harold R., Read, Randy J., Rigden, Daniel J., Rochira, William, Sammito, Massimo, Rodriguez, Filomeno Sanchez, Sheldrick, George M., Shelley, Kathryn L., Simkovic, Felix, Simpkin, Adam J., Skubak, Pavol, Sobolev, Egor, Steiner, Roberto A., Stevenson, Kyle, Tews, Ivo, Thomas, Jens M. H., Thorn, Andrea, Trivino Valls, Josep, Uski, Ville, Uson, Isabel, Vagin, Alexei, Velankar, Sameer, Vollmar, Melanie, Walden, Helen, Waterman, David, Wilson, Keith S., Winn, Martyn D., Winter, Graeme, Wojdyr, Marcin, and Yamashita, Keitaro

Abstract

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world., Funding Agencies|Royal Society [UF160039, URF\R\221006, RGF/R1/181006]; UK Engineering and Physical Sciences Research Council (EPSRC) [EP/R513386/1]; BBSRC [BB/S007105/1, BB/S007083/1, BB/T012935/1, BB/S005099/1, BB/S007040/1]; European Union [871037]; CCP4; Medical Research Council as part of United Kingdom Research and Innovation; UK Research and Innovation: MRC [MC_UP_A025_1012]; European Molecular Biology Laboratory-European Bioinformatics Institute; German Federal Ministry of Education and Research [05K19WWA, 05K22GU5]; Deutsche Forschungsgemeinschaft [TH2135/2-1]; MEYS CR [CZ.02.1.01/0.0/0.0/16_019/0000778]; Czech Academy of Sciences [86652036]; CCP4/STFC [521862101]; iNEXT [653706]; iNEXT-Discovery [871037]; West-Life [675858]; EOSC-Life - Horizon 2020 program of the European Commission [824087]; Netherlands Organization for Scientific Research (NWO) [722.011.011, 723.013.003]; Dutch Cancer Society; Dutch Ministry of Health, Welfare and Sport; Wellcome Trust [209407/Z/17/Z]; Wellcome Trust SRF [200898]; Wellcome Centre for Cell Biology core grant [203149]; STFC-UK/CCP4: Agreement for the integration of methods into the CCP4 software distribution, ARCIMBOLDO_LOW; Spanish MICINN/AEI/FEDER/UE [PID2021-128751NB-I00]; NWOApplied Sciences and Engineering Domain; CCP4 [13337, 16219]; Rontgen Angstrom Cluster [349-2013-597]; SciLifeLab and Wallenberg Data Driven Life Science Program [KAW 2020.0239]; Dutch Research Council (NWO) [VI.Veni.192.143]; EMBO fellowship [ALTF 609-2017]; EPSRC [EP/G037280/1]; BBSRC Institute Strategic Programme Grants [BB/P012523/1, BB/P012574/1]; STFC/CCP4 [7920 S2 2020 007]

Published
2023
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33. Structure and engineering of the minimal type VI CRISPR-Cas13bt3

Author

Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Nakagawa, Ryoya, Kannan, Soumya, Altae-Tran, Han, Takeda, Satoru N, Tomita, Atsuhiro, Hirano, Hisato, Kusakizako, Tsukasa, Nishizawa, Tomohiro, Yamashita, Keitaro, Zhang, Feng, Nishimasu, Hiroshi, Nureki, Osamu, Massachusetts Institute of Technology. Department of Brain and Cognitive Sciences, Nakagawa, Ryoya, Kannan, Soumya, Altae-Tran, Han, Takeda, Satoru N, Tomita, Atsuhiro, Hirano, Hisato, Kusakizako, Tsukasa, Nishizawa, Tomohiro, Yamashita, Keitaro, Zhang, Feng, Nishimasu, Hiroshi, and Nureki, Osamu

Abstract

Type VI CRISPR-Cas13 effector enzymes catalyze RNA-guided RNA cleavage and have been harnessed for various technologies, such as RNA detection, targeting, and editing. Recent studies identified Cas13bt3 (also known as Cas13X.1) as a miniature Cas13 enzyme, which can be used for knockdown and editing of target transcripts in mammalian cells. However, the action mechanism of the compact Cas13bt3 remains unknown. Here, we report the structures of the Cas13bt3-guide RNA complex and the Cas13bt3-guide RNA-target RNA complex. The structures revealed how Cas13bt3 recognizes the guide RNA and its target RNA and provided insights into the activation mechanism of Cas13bt3, which is distinct from those of the other Cas13a/d enzymes. Furthermore, we rationally engineered enhanced Cas13bt3 variants and ultracompact RNA base editors. Overall, this study improves our mechanistic understanding of the CRISPR-Cas13 enzymes and paves the way for the development of efficient Cas13-mediated transcriptome modulation technologies.

Published
2023

34. The CCP4 suite: integrative software for macromolecular crystallography

Author

Royal Society (UK), Engineering and Physical Sciences Research Council (UK), European Commission, Medical Research Council (UK), Federal Ministry of Education and Research (Germany), German Research Foundation, Institute of Geology of the Czech Academy of Sciences, Netherlands Organization for Scientific Research, Dutch Cancer Society, Wellcome Trust, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Agirre, Jon, Atanasova, Mihaela, Bagdonas, Haroldas, Ballard, Charles B., Basle, A., Beilsten-Edmands, James, Borges, Rafael J., Brown, D. G., Burgos-Mármol, J. Javier, Berrisford, J., Bond, Paul S., Caballero, Iracema, Catapano, Lucrezia, Chojnowski, G., Cook, Atlanta G., Cowtan, K., Croll, Tristan I., Debreczeny, Judith E., Devenish, Nicholas E., Dodson, Eleanor J., Drevon, Tarik R., Emsley, Paul, Evans, Gwyndaf, Evans, Phil R., Fando, M., Foadi, James, Fuentes-Montero, Luis, Garman, Elspeth F., Gerstel, Markus, Gildea, Richard J., Hatti, Kaushik, Hekkelman, Maarten L., Heuser, Philipp, Wen Hoh, Soon, Hough, Michael A., Jenkins, Huw T., Jiménez, Elisabet, Joosten, Robbie P., Keegan, R. M., Keep, Nicholas, Krissinel, E., Kolenko, Petr, Kovalevskiy, O., Lamzin, V., Lawson, David M., Lebedev, Andrey, Leslie, A. G. W., Lohkamp, B., Long, Fei, Maly, Martin, McCoy, Airlie J., McNicholas, S., Medina, Ana, Millán, Claudia, Murray, James W., Murshudov, Garib, Nicholls, R. A., Noble, Martin E. M., Oeffner, Robert D., Pannu, Navraj S., Parkhurst, James M., Pearce, Nicholas, Pereira, Joana, Perrakis, Anastassis, Powell, Harold R., Read, Randy J., Rigden, D. J., Rochira, William, Sammito, Massimo, Sánchez Rodríguez, Filomeno, Sheldrick, George M., Shelley, Kathryn L., Simkovic, Felix, Simpkin, A. J., Skubák, P., Sobolev, Egor, Steiner, Roberto A., Stevenson, Kyle, Tews, I., Thomas, J. M. H., Thorn, Andrea, Triviño, Josep, Uski, V., Usón, Isabel, Vagin, Alexei, Velankar, Sameer, Vollmar, Melanie, Walden, Helen, Waterman, David, Wilson, Keith S., Winn, Martyn D., Winter, Graeme, Wojdyr, M., Yamashita, Keitaro, Royal Society (UK), Engineering and Physical Sciences Research Council (UK), European Commission, Medical Research Council (UK), Federal Ministry of Education and Research (Germany), German Research Foundation, Institute of Geology of the Czech Academy of Sciences, Netherlands Organization for Scientific Research, Dutch Cancer Society, Wellcome Trust, Ministerio de Ciencia e Innovación (España), Agencia Estatal de Investigación (España), Agirre, Jon, Atanasova, Mihaela, Bagdonas, Haroldas, Ballard, Charles B., Basle, A., Beilsten-Edmands, James, Borges, Rafael J., Brown, D. G., Burgos-Mármol, J. Javier, Berrisford, J., Bond, Paul S., Caballero, Iracema, Catapano, Lucrezia, Chojnowski, G., Cook, Atlanta G., Cowtan, K., Croll, Tristan I., Debreczeny, Judith E., Devenish, Nicholas E., Dodson, Eleanor J., Drevon, Tarik R., Emsley, Paul, Evans, Gwyndaf, Evans, Phil R., Fando, M., Foadi, James, Fuentes-Montero, Luis, Garman, Elspeth F., Gerstel, Markus, Gildea, Richard J., Hatti, Kaushik, Hekkelman, Maarten L., Heuser, Philipp, Wen Hoh, Soon, Hough, Michael A., Jenkins, Huw T., Jiménez, Elisabet, Joosten, Robbie P., Keegan, R. M., Keep, Nicholas, Krissinel, E., Kolenko, Petr, Kovalevskiy, O., Lamzin, V., Lawson, David M., Lebedev, Andrey, Leslie, A. G. W., Lohkamp, B., Long, Fei, Maly, Martin, McCoy, Airlie J., McNicholas, S., Medina, Ana, Millán, Claudia, Murray, James W., Murshudov, Garib, Nicholls, R. A., Noble, Martin E. M., Oeffner, Robert D., Pannu, Navraj S., Parkhurst, James M., Pearce, Nicholas, Pereira, Joana, Perrakis, Anastassis, Powell, Harold R., Read, Randy J., Rigden, D. J., Rochira, William, Sammito, Massimo, Sánchez Rodríguez, Filomeno, Sheldrick, George M., Shelley, Kathryn L., Simkovic, Felix, Simpkin, A. J., Skubák, P., Sobolev, Egor, Steiner, Roberto A., Stevenson, Kyle, Tews, I., Thomas, J. M. H., Thorn, Andrea, Triviño, Josep, Uski, V., Usón, Isabel, Vagin, Alexei, Velankar, Sameer, Vollmar, Melanie, Walden, Helen, Waterman, David, Wilson, Keith S., Winn, Martyn D., Winter, Graeme, Wojdyr, M., and Yamashita, Keitaro

Abstract

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.

Published
2023

43. Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL

Author

Suga, Michihiro, Akita, Fusamichi, Sugahara, Michihiro, Kubo, Minoru, Nakajima, Yoshiki, Nakane, Takanori, Yamashita, Keitaro, Umena, Yasufumi, Nakabayashi, Makoto, Yamane, Takahiro, Nakano, Takamitsu, Suzuki, Mamoru, Masuda, Tetsuya, Inoue, Shigeyuki, Kimura, Tetsunari, Nomura, Takashi, Yonekura, Shinichiro, Yu, Long-Jiang, Sakamoto, Tomohiro, Motomura, Taiki, Chen, Jing-Hua, Kato, Yuki, Noguchi, Takumi, Tono, Kensuke, Joti, Yasumasa, Kameshima, Takashi, Hatsui, Takaki, Nango, Eriko, Tanaka, Rie, Naitow, Hisashi, Matsuura, Yoshinori, Yamashita, Ayumi, Yamamoto, Masaki, Nureki, Osamu, Yabashi, Makina, Ishikawa, Tetsuya, Iwata, So, and Shen, Jian-Ren

Published
2017
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45. Structural basis for [Na.sup.+] transport mechanism by a light-driven [Na.sup.+] pump

Author

Kato, Hideaki E., Inoue, Keiichi, Abe-Yoshizumi, Rei, Kato, Yoshitaka, Ono, Hikaru, Konno, Masae, Hososhima, Shoko, Ishizuka, Toru, Hoque, Mohammad Razuanul, Kunitomo, Hirofumi, Ito, Jumpei, Yoshizawa, Susumu, Yamashita, Keitaro, Takemoto, Mizuki, Nishizawa, Tomohiro, Taniguchi, Reiya, Kogure, Kazuhiro, Maturana, Andres D., Iino, Yuichi, Yawo, Hiromu, Ishitani, Ryuichiro, Kandori, Hideki, and Nureki, Osamu

Subjects
Biological transport, Active -- Identification and classification, Proteins -- Structure, Sodium channels -- Health aspects -- Identification and classification, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Krokinobacter eikastus rhodopsin 2 (KR2) is the first light-driven [Na.sup.+] pump discovered, and is viewed as a potential next-generation optogenetics tool. Since the positively charged Schiff base proton, located within the ion-conducting pathway of all light-driven ion pumps, was thought to prohibit the transport of a non-proton cation, the discovery of KR2 raised the question of how it achieves [Na.sup.+] transport. Here we present crystal structures of KR2 under neutral and acidic conditions, which represent the resting and M-like intermediate states, respectively. Structural and spectroscopic analyses revealed the gating mechanism, whereby the flipping of Asp116 sequesters the Schiff base proton from the conducting pathway to facilitate [Na.sup.+] transport. Together with the structure-based engineering of the first light-driven [K.sup.+] pumps, electrophysiological assays in mammalian neurons and behavioural assays in a nematode, our studies reveal the molecular basis for light-driven non-proton cation pumps and thus provide a framework that may advance the development of next-generation optogenetics., Many organisms capture light energy and information using the rhodopsin family of proteins, which comprise the heptahelical transmembrane (7-TM) proteins called opsins covalently linked to retinal. Based on their primary [...]

Published
2015
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48. ALS mutations in the TIA-1 prion-like domain trigger highly condensed pathogenic structures

Author

20809652, 70336593, Sekiyama, Naotaka, Takaba, Kiyofumi, Maki-Yonekura, Saori, Akagi, Ken-ichi, Ohtani, Yasuko, Imamura, Kayo, Terakawa, Tsuyoshi, Yamashita, Keitaro, Inaoka, Daigo, Yonekura, Koji, Kodama, Takashi S., Tochio, Hidehito, 20809652, 70336593, Sekiyama, Naotaka, Takaba, Kiyofumi, Maki-Yonekura, Saori, Akagi, Ken-ichi, Ohtani, Yasuko, Imamura, Kayo, Terakawa, Tsuyoshi, Yamashita, Keitaro, Inaoka, Daigo, Yonekura, Koji, Kodama, Takashi S., and Tochio, Hidehito

Published
2022

49. Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine

Author

10314246, Kishi, Koichiro E., Kim, Yoon Seok, Fukuda, Masahiro, Inoue, Masatoshi, Kusakizako, Tsukasa, Wang, Peter Y., Ramakrishnan, Charu, Byrne, Eamon F.X., Thadhani, Elina, Paggi, Joseph M., Matsui, Toshiki E., Yamashita, Keitaro, Nagata, Takashi, Konno, Masae, Quirin, Sean, Lo, Maisie, Benster, Tyler, Uemura, Tomoko, Liu, Kehong, Shibata, Mikihiro, Nomura, Norimichi, Iwata, So, Nureki, Osamu, Dror, Ron O., Inoue, Keiichi, Deisseroth, Karl, Kato, Hideaki E., 10314246, Kishi, Koichiro E., Kim, Yoon Seok, Fukuda, Masahiro, Inoue, Masatoshi, Kusakizako, Tsukasa, Wang, Peter Y., Ramakrishnan, Charu, Byrne, Eamon F.X., Thadhani, Elina, Paggi, Joseph M., Matsui, Toshiki E., Yamashita, Keitaro, Nagata, Takashi, Konno, Masae, Quirin, Sean, Lo, Maisie, Benster, Tyler, Uemura, Tomoko, Liu, Kehong, Shibata, Mikihiro, Nomura, Norimichi, Iwata, So, Nureki, Osamu, Dror, Ron O., Inoue, Keiichi, Deisseroth, Karl, and Kato, Hideaki E.

Abstract

ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsins; mechanisms for passive channel conduction in this family have remained mysterious. Here, we present the 2.0 Å resolution cryo-EM structure of ChRmine, revealing architectural features atypical for channelrhodopsins: trimeric assembly, a short transmembrane-helix 3, a twisting extracellular-loop 1, large vestibules within the monomer, and an opening at the trimer interface. We applied this structure to design three proteins (rsChRmine and hsChRmine, conferring further red-shifted and high-speed properties, respectively, and frChRmine, combining faster and more red-shifted performance) suitable for fundamental neuroscience opportunities. These results illuminate the conduction and gating of pump-like channelrhodopsins and point the way toward further structure-guided creation of channelrhodopsins for applications across biology.

Published
2022

50. Native structure of photosystem II at 1.95 Å resolution viewed by femtosecond X-ray pulses

Author

Suga, Michihiro, Akita, Fusamichi, Hirata, Kunio, Ueno, Go, Murakami, Hironori, Nakajima, Yoshiki, Shimizu, Tetsuya, Yamashita, Keitaro, Yamamoto, Masaki, Ago, Hideo, and Shen, Jian-Ren

Subjects
Photosynthesis -- Methods, Photosystem II -- Observations -- Structure, Environmental issues, Science and technology, Zoology and wildlife conservation
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 angstrom resolution, which revealed that the OEC is a [Mn.sub.4]Ca[O.sub.5]-cluster coordinated by a well defined protein environment (1). However, extended X-ray absorption fine structure (EXAFS) studies showed that the manganese cations in the OEC are easily reduced by X-ray irradiation (2), and slight differences were found in the Mn-Mn distances determined by XRD (1), EXAFS (3-7) and theoretical studies (8-14). Here we report a 'radiation-damage-free' structure of PSII from Thermosynechococcus vulcanusin the [S.sub.1] state at a resolution of 1.95 angstroms using femtosecond X-ray pulses of the SPring-8 angstrom 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 angstroms. The valences of each manganese atom were tentatively assigned as Mn1D(m), 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., PSII is a multi-subunit pigment-protein complex embedded in the thylakoid membranes of higher plants, green algae and cyanobacteria, and is the only molecular machine capable of oxidizing water by use [...]

Published
2015
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