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416 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 more...

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. more...

Published
2024

2. 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 more...

Published
2024
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4. Generalized Graph Signal Sampling by Difference-of-Convex Optimization

Author

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

Subjects
Electrical Engineering and Systems Science - Signal Processing
Abstract

We propose a desigining method of a flexible sampling operator for graph signals via a difference-of-convex (DC) optimization algorithm. A fundamental challenge in graph signal processing is sampling, especially for graph signals that are not bandlimited. In order to sample beyond bandlimited graph signals, there are studies to expand the generalized sampling theory for the graph setting. Vertex-wise sampling and flexible sampling are two main strategies to sample graph signals. Recovery accuracy of existing vertex-wise sampling methods is highly dependent on specific vertices selected to generate a sampled graph signal that may compromise the accurary especially when noise is generated at the vertices. In contrast, a flexible sampling mixes values at multiple vertices to generate a sampled signal for robust sampling; however, existing flexible sampling methods impose strict assumptions and aggressive relaxations. To address these limitations, we aim to design a flexible sampling operator without such strict assumptions and aggressive relaxations by introducing DC optimization. By formulating the problem of designing a flexible sampling operator as a DC optimization problem, our method ensures robust sampling for graph signals under arbitrary priors based on generalized sampling theory. We develop an efficient solver based on the general double-proximal gradient DC algorithm, which guarantees convergence to a critical point. Experimental results demonstrate the superiority of our method in sampling and recovering beyond bandlimited graph signals compared to existing approaches., Comment: Submitted to the IEEE Transactions on Signal Processing more...

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. more...

Published
2023
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11. Structural basis of anticancer drug recognition and amino acid transport by LAT1.

Author

Lee, Yongchan, Jin, Chunhuan, Ohgaki, Ryuichi, Xu, Minhui, Ogasawara, Satoshi, Warshamanage, Rangana, Yamashita, Keitaro, Murshudov, Garib, Nureki, Osamu, Murata, Takeshi, and Kanai, Yoshikatsu

Subjects
AMINO acid transport, LIFE sciences, BIOCHEMICAL substrates, LIGANDS (Biochemistry), DRUG design, MELPHALAN
Abstract

LAT1 (SLC7A5) transports large neutral amino acids and plays pivotal roles in cancer proliferation, immune response and drug delivery. Despite recent advances in structural understanding of LAT1, how it discriminates substrates and inhibitors including the clinically relevant drugs remains elusive. Here we report six structures of LAT1 across three conformations with bound ligands, elucidating its substrate transport and inhibitory mechanisms. JPH203 (also known as nanvuranlat or KYT-0353), an anticancer drug in clinical trials, traps LAT1 in an outward-facing state with a U-shaped conformer, with its amino-phenylbenzoxazol moiety pushing against transmembrane helix 3 (TM3) and bending TM10. Physiological substrates like ʟ-Phe lack such effects, whereas melphalan poses steric hindrance, explaining its inhibitory activity. The "classical" system L inhibitor BCH induces an occluded state critical for transport, confirming its substrate-like behavior. These findings provide a structural basis for substrate recognition and inhibition of LAT1, guiding future drug design. Lee et al. report six cryo-EM structures of LAT1 in complex with various substrates and inhibitors, including nanvuranlat (JPH203) under clinical trials. These structures provide insights into the mechanisms of amino acid transport and inhibition, aiding future drug design. [ABSTRACT FROM AUTHOR] more...

Published
2025
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13. 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 more...

Published
2021

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. more...

Published
2022
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25. 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] more...

Published
2024
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26. 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 more...

Published
2019

28. 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 more...

Published
2024
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30. Crystal structure of heliorhodopsin

Author

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

Subjects
Structure, Analysis, Crystal structure -- Analysis, Rhodopsin -- Structure, Crystals -- Structure
Abstract

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 [...], 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. more...

Published
2019
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31. 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 more...

Published
2018
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32. 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 more...

Published
2023
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35. 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 more...

Published
2020
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36. 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 more...

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. more...

Published
2023

37. 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
Research, Structure, Chemical properties, Crystal structure -- Research, Rhodopsin -- Structure -- Chemical properties, Neurons
Abstract

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] , [...], 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. more...

Published
2018
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42. 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 more...

Published
2020
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43. 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 more...

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] more...

Published
2023
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44. 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 more...

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. more...

Published
2023

45. 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 more...

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. more...

Published
2023

46. 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 more...

Published
2023
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49. Abundant Aβ fibrils in ultracentrifugal supernatants of aqueous extracts from Alzheimer’s disease brains

Author

Stern, Andrew M., primary, Yang, Yang, additional, Jin, Shanxue, additional, Yamashita, Keitaro, additional, Meunier, Angela L., additional, Liu, Wen, additional, Cai, Yuqi, additional, Ericsson, Maria, additional, Liu, Lei, additional, Goedert, Michel, additional, Scheres, Sjors H.W., additional, and Selkoe, Dennis J., additional more...

Published
2023
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