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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. Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

Author

Lawson, Catherine L., Kryshtafovych, Andriy, Pintilie, Grigore D., Burley, Stephen K., Černý, Jiří, Chen, Vincent B., Emsley, Paul, Gobbi, Alberto, Joachimiak, Andrzej, Noreng, Sigrid, Prisant, Michael G., Read, Randy J., Richardson, Jane S., Rohou, Alexis L., Schneider, Bohdan, Sellers, Benjamin D., Shao, Chenghua, Sourial, Elizabeth, Williams, Chris I., Williams, Christopher J., Yang, Ying, Abbaraju, Venkat, Afonine, Pavel V., Baker, Matthew L., Bond, Paul S., Blundell, Tom L., Burnley, Tom, Campbell, Arthur, Cao, Renzhi, Cheng, Jianlin, Chojnowski, Grzegorz, Cowtan, K. D., DiMaio, Frank, Esmaeeli, Reza, Giri, Nabin, Grubmüller, Helmut, Hoh, Soon Wen, Hou, Jie, Hryc, Corey F., Hunte, Carola, Igaev, Maxim, Joseph, Agnel P., Kao, Wei-Chun, Kihara, Daisuke, Kumar, Dilip, Lang, Lijun, Lin, Sean, Maddhuri Venkata Subramaniya, Sai R., Mittal, Sumit, Mondal, Arup, Moriarty, Nigel W., Muenks, Andrew, Murshudov, Garib N., Nicholls, Robert A., Olek, Mateusz, Palmer, Colin M., Perez, Alberto, Pohjolainen, Emmi, Pothula, Karunakar R., Rowley, Christopher N., Sarkar, Daipayan, Schäfer, Luisa U., Schlicksup, Christopher J., Schröder, Gunnar F., Shekhar, Mrinal, Si, Dong, Singharoy, Abhishek, Sobolev, Oleg V., Terashi, Genki, Vaiana, Andrea C., Vedithi, Sundeep C., Verburgt, Jacob, Wang, Xiao, Warshamanage, Rangana, Winn, Martyn D., Weyand, Simone, Yamashita, Keitaro, Zhao, Minglei, Schmid, Michael F., Berman, Helen M., and Chiu, Wah

Published
2024
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4. 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

7. 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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11. 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

13. Improving macromolecular structure refinement with metal‐coordination restraints.

Author

Babai, Kaveh H., Long, Fei, Malý, Martin, Yamashita, Keitaro, and Murshudov, Garib N.

Subjects
BOND angles, CHEMICAL bond lengths, LIBRARY cooperation, DATABASES, CRYSTALLOGRAPHY
Abstract

Metals are essential components for the structure and function of many proteins. However, accurate modelling of their coordination environments remains a challenge due to the complexity and diversity of metal‐coordination geometries. To address this, a method is presented for extracting and analysing coordination information, including bond lengths and angles, from the Crystallography Open Database. By using these data, comprehensive descriptions of metal‐containing components are generated. A stereochemical information generator for a particular component within a specific macromolecule leverages an example PDB/mmCIF file containing the component to account for the actual surrounding environment. A matching process has been developed and implemented to align the derived metal structures with idealized coordinates from a coordination geometry library. Additionally, various strategies, depending on the quality of the matches, were employed to compile distance and angle statistics for the refinement of macromolecular structures. The developed methods were implemented in a new program, MetalCoord, that classifies and utilizes the metal‐coordination geometry. The effectiveness of the developed algorithms was tested using metal‐containing components from the PDB. As a result, metal‐containing components from the CCP4 monomer library have been updated. The updated monomer dictionaries, in concert with the derived restraints, can be used in most structural biology computations, including macromolecular crystallography, single‐particle cryo‐EM and even molecular mechanics. [ABSTRACT FROM AUTHOR]

Published
2024
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15. 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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23. 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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25. An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser

Author

Suga, Michihiro, Akita, Fusamichi, Yamashita, Keitaro, Nakajima, Yoshiki, Ueno, Go, Li, Hongjie, Yamane, Takahiro, Hirata, Kunio, Umena, Yasufumi, Yonekura, Shinichiro, Yu, Long-Jiang, Murakami, Hironori, Nomura, Takashi, Kimura, Tetsunari, Kubo, Minoru, Baba, Seiki, Kumasaka, Takashi, Tono, Kensuke, Yabashi, Makina, Isobe, Hiroshi, Yamaguchi, Kizashi, Yamamoto, Masaki, Ago, Hideo, and Shen, Jian-Ren

Published
2019

27. Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge

Author

Lawson, Catherine, primary, Kryshtafovych, Andriy, additional, Pintilie, Grigore, additional, Burley, Stephen, additional, Cerny, Jiri, additional, Chen, Vincent, additional, Emsley, Paul, additional, Gobbi, Alberto, additional, Joachimiak, Andrzej, additional, Noreng, Sigrid, additional, Prisant, Michael, additional, Read, Randy, additional, Richardson, Jane, additional, Rohou, Alexis, additional, Schneider, Bohdan, additional, Sellers, Benjamin, additional, Chao, Chenghua, additional, Sourial, Elizabeth, additional, Williams, Chris, additional, Williams, Christopher, additional, Yang, Ying, additional, Abbaraju, Venkat, additional, Afonine, Pavel V., additional, Baker, Matthew, additional, Bond, Paul, additional, Blundell, Tom, additional, Burnley, Tom, additional, Campbell, Arthur, additional, Cao, Renzhi, additional, Cheng, Jianlin, additional, Chojnowski, Grzegorz, additional, Cowtan, Kevin, additional, Dimaio, Frank, additional, Esmaeeli, Reza, additional, Giri, Nabin, additional, Grubmüller, Helmut, additional, Hoh, Soon Wen, additional, Hou, Jie, additional, Hryc, Corey, additional, Hunte, Carola, additional, Igaev, Maxim, additional, Joseph, Agnel, additional, Kao, Wei-Chun, additional, Kihara, Daisuke, additional, Kumar, Dilip, additional, Lang, Lijun, additional, Lin, Sean, additional, Subramaniya, Sai Raghavendra Maddhuri Venkata, additional, Mittal, Sumit, additional, Mondal, Arup, additional, Moriarty, Nigel, additional, Muenks, Andrew, additional, Murshudov, Garib, additional, Nicholls, Robert, additional, Olek, Mateusz, additional, Palmer, Colin, additional, Perez, Alberto, additional, Pohjolainen, Emmi, additional, Pothula, Karunakar, additional, Rowley, Christopher, additional, Sarkar, Daipayan, additional, Schäfer, Luisa, additional, Schlicksup, Christopher, additional, Schroeder, Gunnar, additional, Shekhar, Mrinal, additional, Si, Dong, additional, Singharoy, Abhishek, additional, Sobolev, Oleg, additional, Terashi, Genki, additional, Vaiana, Andrea, additional, Vedithi, Sundeep, additional, Verburgt, Jacob, additional, Wang, Xiao, additional, Warshamanage, Rangana, additional, Winn, Martyn, additional, Weyand, Simone, additional, Yamashita, Keitaro, additional, Zhao, Minglei, additional, Schmid, Michael, additional, Berman, Helen, additional, and Chiu, Wah, additional

Published
2024
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29. 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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31. 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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32. 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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33. GEMMI and Servalcat restrain REFMAC5

Author

Yamashita, Keitaro, Wojdyr, Marcin, Long, Fei, Nicholls, Robert A, Murshudov, Garib N, Yamashita, Keitaro [0000-0002-5442-7582], Wojdyr, Marcin [0000-0003-3980-4092], Long, Fei [0000-0002-2553-9841], Nicholls, Robert A [0000-0002-8577-8617], Murshudov, Garib N [0000-0001-6483-3587], and Apollo - University of Cambridge Repository

Subjects
Models, Molecular, Macromolecular Substances, Protein Conformation, GEMMI, Proteins, Servalcat, model refinement, Crystallography, X-Ray, REFMAC5, Software
Abstract

Macromolecular refinement uses experimental data together with prior chemical knowledge (usually digested into geometrical restraints) to optimally fit an atomic structural model into experimental data, while ensuring that the model is chemically plausible. In the CCP4 suite this chemical knowledge is stored in a Monomer Library, which comprises a set of restraint dictionaries. To use restraints in refinement, the model is analysed and template restraints from the dictionary are used to infer (i) restraints between concrete atoms and (ii) the positions of riding hydrogen atoms. Recently, this mundane process has been overhauled. This was also an opportunity to enhance the Monomer Library with new features, resulting in a small improvement in REFMAC5 refinement. Importantly, the overhaul of this part of CCP4 has increased flexibility and eased experimentation, opening up new possibilities.

Published
2023

36. 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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37. 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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38. 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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41. The CCP4 suite: integrative software for macromolecular crystallography

Author

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

Published
2023
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46. 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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47. 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

48. 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

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