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      Cryo-EM structure of an active central apparatus

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          Abstract

          Accurately regulated ciliary beating in time and space is critical for diverse cellular activities, which impact the survival and development of nearly all eukaryotic species. An essential beating regulator is the conserved central apparatus (CA) of motile cilia, composed of a pair of microtubules (C1 and C2) associated with hundreds of protein subunits per repeating unit. It is largely unclear how the CA plays its regulatory roles in ciliary motility. Here, we present high-resolution structures of Chlamydomonas reinhardtii CA by cryo-electron microscopy (cryo-EM) and its dynamic conformational behavior at multiple scales. The structures show how functionally related projection proteins of CA are clustered onto a spring-shaped scaffold of armadillo-repeat proteins, facilitated by elongated rachis-like proteins. The two halves of the CA are brought together by elastic chain-like bridge proteins to achieve coordinated activities. We captured an array of kinesin-like protein (KLP1) in two different stepping states, which are actively correlated with beating wave propagation of cilia. These findings establish a structural framework for understanding the role of the CA in cilia.

          Abstract

          Here, authors solve cryo-EM structures of the central apparatus of motile cilia and analyze its dynamic conformations to elucidate the mechanism of ciliary beating.

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          Fiji: an open-source platform for biological-image analysis.

          Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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            UCSF Chimera--a visualization system for exploratory research and analysis.

            The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. Copyright 2004 Wiley Periodicals, Inc.
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              cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

              A software tool, cryoSPARC, addresses the speed bottleneck in cryo-EM image processing, enabling automated macromolecular structure determination in hours on a desktop computer without requiring a starting model.
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                Author and article information

                Contributors
                jack.zhang@yale.edu
                Journal
                Nat Struct Mol Biol
                Nat Struct Mol Biol
                Nature Structural & Molecular Biology
                Nature Publishing Group US (New York )
                1545-9993
                1545-9985
                16 May 2022
                16 May 2022
                2022
                : 29
                : 5
                : 472-482
                Affiliations
                [1 ]GRID grid.47100.32, ISNI 0000000419368710, Department of Molecular Biophysics and Biochemistry, , Yale University, ; New Haven, CT USA
                [2 ]GRID grid.418021.e, ISNI 0000 0004 0535 8394, Present Address: Center for Molecular Microscopy, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, National Institutes of Health, ; Frederick, MD USA
                Author information
                http://orcid.org/0000-0001-9702-978X
                http://orcid.org/0000-0001-9625-9313
                http://orcid.org/0000-0001-8617-2855
                Article
                769
                10.1038/s41594-022-00769-9
                9113940
                35578022
                6819af03-2c8f-43fc-97b9-5febf886cb6d
                © The Author(s) 2022

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 16 September 2021
                : 30 March 2022
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                © The Author(s), under exclusive licence to Springer Nature America, Inc. 2022

                Molecular biology
                cryoelectron microscopy,cilia,kinesin,motility
                Molecular biology
                cryoelectron microscopy, cilia, kinesin, motility

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