1
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Pintscher S, Pietras R, Mielecki B, Szwalec M, Wójcik-Augustyn A, Indyka P, Rawski M, Koziej Ł, Jaciuk M, Ważny G, Glatt S, Osyczka A. Molecular basis of plastoquinone reduction in plant cytochrome b 6f. NATURE PLANTS 2024:10.1038/s41477-024-01804-x. [PMID: 39362993 DOI: 10.1038/s41477-024-01804-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 09/03/2024] [Indexed: 10/05/2024]
Abstract
A multi-subunit enzyme, cytochrome b6f (cytb6f), provides the crucial link between photosystems I and II in the photosynthetic membranes of higher plants, transferring electrons between plastoquinone (PQ) and plastocyanin. The atomic structure of cytb6f is known, but its detailed catalytic mechanism remains elusive. Here we present cryogenic electron microscopy structures of spinach cytb6f at 1.9 Å and 2.2 Å resolution, revealing an unexpected orientation of the substrate PQ in the haem ligand niche that forms the PQ reduction site (Qn). PQ, unlike Qn inhibitors, is not in direct contact with the haem. Instead, a water molecule is coordinated by one of the carbonyl groups of PQ and can act as the immediate proton donor for PQ. In addition, we identify water channels that connect Qn with the aqueous exterior of the enzyme, suggesting that the binding of PQ in Qn displaces water through these channels. The structures confirm large movements of the head domain of the iron-sulfur protein (ISP-HD) towards and away from the plastoquinol oxidation site (Qp) and define the unique position of ISP-HD when a Qp inhibitor (2,5-dibromo-3-methyl-6-isopropylbenzoquinone) is bound. This work identifies key conformational states of cytb6f, highlights fundamental differences between substrates and inhibitors and proposes a quinone-water exchange mechanism.
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Affiliation(s)
- Sebastian Pintscher
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Plant Biotechnology, Jagiellonian University, Kraków, Poland
| | - Rafał Pietras
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Molecular Biophysics, Jagiellonian University, Kraków, Poland
| | - Bohun Mielecki
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Molecular Biophysics, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Mateusz Szwalec
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Molecular Biophysics, Jagiellonian University, Kraków, Poland
| | - Anna Wójcik-Augustyn
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Molecular Biophysics, Jagiellonian University, Kraków, Poland
| | - Paulina Indyka
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Kraków, Poland
| | - Michał Rawski
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Kraków, Poland
| | - Łukasz Koziej
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
| | - Marcin Jaciuk
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Kraków, Poland
| | - Grzegorz Ważny
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Kraków, Poland
| | - Sebastian Glatt
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland.
- Department for Biological Sciences and Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria.
| | - Artur Osyczka
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Molecular Biophysics, Jagiellonian University, Kraków, Poland.
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2
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Abe KM, Li G, He Q, Grant T, Lim CJ. Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing. Nat Commun 2024; 15:7705. [PMID: 39231985 PMCID: PMC11375022 DOI: 10.1038/s41467-024-52091-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 08/27/2024] [Indexed: 09/06/2024] Open
Abstract
Air-water interface (AWI) interactions during cryo-electron microscopy (cryo-EM) sample preparation cause significant sample loss, hindering structural biology research. Organisms like nematodes and tardigrades produce Late Embryogenesis Abundant (LEA) proteins to withstand desiccation stress. Here we show that these LEA proteins, when used as additives during plunge freezing, effectively mitigate AWI damage to fragile multi-subunit molecular samples. The resulting high-resolution cryo-EM maps are comparable to or better than those obtained using existing AWI damage mitigation methods. Cryogenic electron tomography reveals that particles are localized at specific interfaces, suggesting LEA proteins form a barrier at the AWI. This interaction may explain the observed sample-dependent preferred orientation of particles. LEA proteins offer a simple, cost-effective, and adaptable approach for cryo-EM structural biologists to overcome AWI-related sample damage, potentially revitalizing challenging projects and advancing the field of structural biology.
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Affiliation(s)
- Kaitlyn M Abe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gan Li
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Qixiang He
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Timothy Grant
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- John and Jeanne Rowe Center for Research in Virology, Morgridge Institute for Research, Madison, WI, 53715, USA
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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3
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Chan LM, Courteau BJ, Maker A, Wu M, Basanta B, Mehmood H, Bulkley D, Joyce D, Lee BC, Mick S, Czarnik C, Gulati S, Lander GC, Verba KA. High-resolution single-particle imaging at 100-200 keV with the Gatan Alpine direct electron detector. J Struct Biol 2024; 216:108108. [PMID: 38944401 DOI: 10.1016/j.jsb.2024.108108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/03/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
Developments in direct electron detector technology have played a pivotal role in enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory and recent experiments indicate advantages to imaging at 100 keV, energies for which the current detectors have not been optimized. In this study, we evaluated the Gatan Alpine detector, designed for operation at 100 and 200 keV. Compared to the Gatan K3, Alpine demonstrated a significant DQE improvement at these energies, specifically a ∼ 4-fold improvement at Nyquist at 100 keV. In single-particle cryo-EM experiments, Alpine datasets yielded better than 2 Å resolution reconstructions of apoferritin at 120 and 200 keV on a ThermoFisher Scientific (TFS) Glacios microscope fitted with a non-standard SP-Twin lens. We also achieved a ∼ 3.2 Å resolution reconstruction of a 115 kDa asymmetric protein complex, proving Alpine's effectiveness with complex biological samples. In-depth analysis revealed that Alpine reconstructions are comparable to K3 reconstructions at 200 keV, and remarkably, reconstruction from Alpine at 120 keV on a TFS Glacios surpassed all but the 300 keV data from a TFS Titan Krios with GIF/K3. Additionally, we show Alpine's capability for high-resolution data acquisition and screening on lower-end systems by obtaining ∼ 3 Å resolution reconstructions of apoferritin and aldolase at 100 keV and detailed 2D averages of a 55 kDa sample using a side-entry cryo holder. Overall, we show that Gatan Alpine performs well with the standard 200 keV imaging systems and may potentially capture the benefits of lower accelerating voltages, bringing smaller sized particles within the scope of cryo-EM.
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Affiliation(s)
- Lieza M Chan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Brandon J Courteau
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Allison Maker
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Hev Mehmood
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - David Bulkley
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States
| | | | | | | | | | | | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States.
| | - Kliment A Verba
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States.
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4
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Urzhumtseva L, Barchet C, Klaholz BP, Urzhumtsev AG. Program VUE: analysing distributions of cryo-EM projections using uniform spherical grids. J Appl Crystallogr 2024; 57:865-876. [PMID: 38846771 PMCID: PMC11151668 DOI: 10.1107/s1600576724002383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 03/12/2024] [Indexed: 06/09/2024] Open
Abstract
Three-dimensional cryo electron microscopy reconstructions are obtained by extracting information from a large number of projections of the object. These projections correspond to different 'views' or 'orientations', i.e. directions in which these projections show the reconstructed object. Uneven distribution of these views and the presence of dominating preferred orientations may distort the reconstructed spatial images. This work describes the program VUE (views on uniform grids for cryo electron microscopy), designed to study such distributions. Its algorithms, based on uniform virtual grids on a sphere, allow an easy calculation and accurate quantitative analysis of the frequency distribution of the views. The key computational element is the Lambert azimuthal equal-area projection of a spherical uniform grid onto a disc. This projection keeps the surface area constant and represents the frequency distribution with no visual bias. Since it has multiple tunable parameters, the program is easily adaptable to individual needs, and to the features of a particular project or of the figure to be produced. It can help identify problems related to an uneven distribution of views. Optionally, it can modify the list of projections, distributing the views more uniformly. The program can also be used as a teaching tool.
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Affiliation(s)
- Ludmila Urzhumtseva
- Architecture et Réactivité de l’ARN, UPR 9002 CNRS, IBMC, Université de Strasbourg, 15 rue R. Descartes, 67084 Strasbourg, France
| | - Charles Barchet
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104, Institut National de la Santé de la Recherche Médicale (Inserm) U964, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Bruno P. Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104, Institut National de la Santé de la Recherche Médicale (Inserm) U964, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Alexandre G. Urzhumtsev
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre National de la Recherche Scientifique (CNRS) UMR 7104, Institut National de la Santé de la Recherche Médicale (Inserm) U964, Université de Strasbourg, 1 rue Laurent Fries, 67404 Illkirch, France
- Université de Lorraine, Physics Department, 54506 Vandoeuvre-lès-Nancy, France
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5
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Kung JE, Johnson MC, Jao CC, Arthur CP, Tegunov D, Rohou A, Sudhamsu J. Disulfi de constrained Fabs overcome target size limitation for high-resolution single-particle cryo-EM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.10.593593. [PMID: 38798381 PMCID: PMC11118328 DOI: 10.1101/2024.05.10.593593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
High-resolution structures of proteins are critical to understanding molecular mechanisms of biological processes and in the discovery of therapeutic molecules. Cryo-EM has revolutionized structure determination of large proteins and their complexes1, but a vast majority of proteins that underlie human diseases are small (< 50 kDa) and usually beyond its reach due to low signal-to-noise images and difficulties in particle alignment2. Current strategies to overcome this problem increase the overall size of small protein targets using scaffold proteins that bind to the target, but are limited by inherent flexibility and not being bound to their targets in a rigid manner, resulting in the target being poorly resolved compared to the scaffolds3-11. Here we present an iteratively engineered molecular design for transforming Fabs (antibody fragments), into conformationally rigid scaffolds (Rigid-Fabs) that, when bound to small proteins (~20 kDa), can enable high-resolution structure determination using cryo-EM. This design introduces multiple disulfide bonds at strategic locations, generates a well-folded Fab constrained into a rigid conformation and can be applied to Fabs from various species, isotypes and chimeric Fabs. We present examples of the Rigid Fab design enabling high-resolution (2.3-2.5 Å) structures of small proteins, Ang2 (26 kDa) and KRAS (21 kDa) by cryo-EM. The strategies for designing disulfide constrained Rigid Fabs in our work thus establish a general approach to overcome the target size limitation of single particle cryo-EM.
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Affiliation(s)
- Jennifer E. Kung
- Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Matthew C. Johnson
- Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Christine C. Jao
- Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Christopher P. Arthur
- Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Dimitry Tegunov
- Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Alexis Rohou
- Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA
| | - Jawahar Sudhamsu
- Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA
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6
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Sauer PV, Cupellini L, Sutter M, Bondanza M, Domínguez Martin MA, Kirst H, Bína D, Koh AF, Kotecha A, Greber BJ, Nogales E, Polívka7 T, Mennucci B, Kerfeld CA. Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. SCIENCE ADVANCES 2024; 10:eadk7535. [PMID: 38578996 PMCID: PMC10997198 DOI: 10.1126/sciadv.adk7535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024]
Abstract
Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria.
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Affiliation(s)
- Paul V. Sauer
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - María Agustina Domínguez Martin
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Henning Kirst
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Bína
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | | | | | - Basil J. Greber
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
| | - Tomáš Polívka7
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Thermo Fisher Scientific, Eindhoven, Netherlands
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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7
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Premageetha GT, Vinothkumar KR, Bose S. Exploring advances in single particle CryoEM with apoferritin: From blobs to true atomic resolution. Int J Biochem Cell Biol 2024; 169:106536. [PMID: 38307321 DOI: 10.1016/j.biocel.2024.106536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/04/2024]
Abstract
Deciphering the three-dimensional structures of macromolecules is of paramount importance for gaining insights into their functions and roles in human health and disease. Single particle cryoEM has emerged as a powerful technique that enables direct visualization of macromolecules and their complexes, and through subsequent averaging, achieve near atomic-level resolution. A major breakthrough was recently achieved with the determination of the apoferritin structure at true atomic resolution. In this review, we discuss the latest technological innovations across the entire single-particle workflow, which have been instrumental in driving the resolution revolution and in transforming cryoEM as a mainstream technique in structural biology. We illustrate these advancements using apoferritin as an example that has served as an excellent benchmark sample for assessing emerging technologies. We further explore whether the existing technology can routinely generate atomic structures of dynamic macromolecules that more accurately represent real-world samples, the limitations in the workflow, and the current approaches employed to overcome them.
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Affiliation(s)
- Gowtham ThambraRajan Premageetha
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bangalore 560065, India; Manipal Academy of Higher Education, Tiger Circle Road, Manipal, Karnataka 576104, India.
| | - Kutti R Vinothkumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Post, Bangalore 560065, India
| | - Sucharita Bose
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bangalore 560065, India.
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8
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Dai Z, Liang L, Wang W, Zuo P, Yu S, Liu Y, Zhao X, Lu Y, Jin Y, Zhang F, Ding D, Deng W, Yin Y. Structural insights into the ubiquitylation strategy of the oligomeric CRL2 FEM1B E3 ubiquitin ligase. EMBO J 2024; 43:1089-1109. [PMID: 38360992 PMCID: PMC10943247 DOI: 10.1038/s44318-024-00047-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Cullin-RING E3 ubiquitin ligase (CRL) family members play critical roles in numerous biological processes and diseases including cancer and Alzheimer's disease. Oligomerization of CRLs has been reported to be crucial for the regulation of their activities. However, the structural basis for its regulation and mechanism of its oligomerization are not fully known. Here, we present cryo-EM structures of oligomeric CRL2FEM1B in its unneddylated state, neddylated state in complex with BEX2 as well as neddylated state in complex with FNIP1/FLCN. These structures reveal that asymmetric dimerization of N8-CRL2FEM1B is critical for the ubiquitylation of BEX2 while FNIP1/FLCN is ubiquitylated by monomeric CRL2FEM1B. Our data present an example of the asymmetric homo-dimerization of CRL. Taken together, this study sheds light on the ubiquitylation strategy of oligomeric CRL2FEM1B according to substrates with different scales.
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Affiliation(s)
- Zonglin Dai
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ling Liang
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Weize Wang
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Peng Zuo
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Shang Yu
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yaqi Liu
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Xuyang Zhao
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yishuo Lu
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yan Jin
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Fangting Zhang
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Dian Ding
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Weiwei Deng
- Department of Mechanics and Aerospace Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuxin Yin
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
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9
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Chan LM, Courteau BJ, Maker A, Wu M, Basanta B, Mehmood H, Bulkley D, Joyce D, Lee BC, Mick S, Gulati S, Lander GC, Verba KA. High-resolution single-particle imaging at 100-200 keV with the Gatan Alpine direct electron detector. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580363. [PMID: 38405886 PMCID: PMC10888765 DOI: 10.1101/2024.02.14.580363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Developments in direct electron detector technology have played a pivotal role in enabling high-resolution structural studies by cryo-EM at 200 and 300 keV. Yet, theory and recent experiments indicate advantages to imaging at 100 keV, energies for which the current detectors have not been optimized. In this study, we evaluated the Gatan Alpine detector, designed for operation at 100 and 200 keV. Compared to the Gatan K3, Alpine demonstrated a significant DQE improvement at these voltages, specifically a ~4-fold improvement at Nyquist at 100 keV. In single-particle cryo-EM experiments, Alpine datasets yielded better than 2 Å resolution reconstructions of apoferritin at 120 and 200 keV on a ThermoFisher Scientific (TFS) Glacios microscope. We also achieved a ~3.2 Å resolution reconstruction for a 115 kDa asymmetric protein complex, proving its effectiveness with complex biological samples. In-depth analysis revealed that Alpine reconstructions are comparable to K3 reconstructions at 200 keV, and remarkably, reconstruction from Alpine at 120 keV on a TFS Glacios surpassed all but the 300 keV data from a TFS Titan Krios with GIF/K3. Additionally, we show Alpine's capability for high-resolution data acquisition and screening on lower-end systems by obtaining ~3 Å resolution reconstructions of apoferritin and aldolase at 100 keV and detailed 2D averages of a 55 kDa sample using a side-entry cryo holder. Overall, we show that Gatan Alpine performs well with the standard 200 keV imaging systems and may potentially capture the benefits of lower accelerating voltages, possibly bringing smaller sized particles within the scope of cryo-EM.
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Affiliation(s)
- Lieza M Chan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Brandon J Courteau
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Allison Maker
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - Mengyu Wu
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Hevatib Mehmood
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
| | - David Bulkley
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, United States
| | | | | | | | | | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92024, United States
| | - Kliment A Verba
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, United States
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10
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Abe KM, Lim CJ. Small LEA proteins as an effective air-water interface protectant for fragile samples during cryo-EM grid plunge freezing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579238. [PMID: 38370693 PMCID: PMC10871254 DOI: 10.1101/2024.02.06.579238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Sample loss due to air-water interface (AWI) interactions is a significant challenge during cryo-electron microscopy (cryo-EM) sample grid plunge freezing. We report that small Late Embryogenesis Abundant (LEA) proteins, which naturally bind to AWI, can protect samples from AWI damage during plunge freezing. This protection is demonstrated with two LEA proteins from nematodes and tardigrades, which rescued the cryo-EM structural determination outcome of two fragile multisubunit protein complexes.
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Affiliation(s)
- Kaitlyn M. Abe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706
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11
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Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Đorđević-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. Overcoming resolution attenuation during tilted cryo-EM data collection. Nat Commun 2024; 15:389. [PMID: 38195598 PMCID: PMC10776679 DOI: 10.1038/s41467-023-44555-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024] Open
Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation, containing an unnatural nucleotide for studying novel base pair recognition. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle during data acquisition. These results reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
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Affiliation(s)
- Sriram Aiyer
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Philip R Baldwin
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shi Min Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore
| | - Zelin Shan
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- College of Pharmacy, Kyung Hee University, Seoul, 02247, Republic of Korea
| | - Atousa Mehrani
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Marianne E Bowman
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Gordon Louie
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Dario Oliveira Passos
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | | | - Mario Mietzsch
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Joshua A Hull
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Benjamin A Barad
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Robert McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Mavis Agbandje-McKenna
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Blvd Box 7, Alachua, FL, 32615, USA
| | - Joseph A P Noel
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, 16 Science Drive 4, Singapore, 117558, Singapore.
- Disease Intervention Technology Laboratory (DITL), Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Singapore, 138648, Singapore.
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Republic of Singapore.
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA, 92093, USA.
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12
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Wilhelm CA, Mallik L, Kelly AL, Brotzman S, Mendoza J, Anders AG, Leskaj S, Castillo C, Ruotolo BT, Cianfrocco MA, Koutmos M. Bacterial RNA-free RNase P: Structural and functional characterization of multiple oligomeric forms of a minimal protein-only ribonuclease P. J Biol Chem 2023; 299:105327. [PMID: 37806495 PMCID: PMC10652100 DOI: 10.1016/j.jbc.2023.105327] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023] Open
Abstract
tRNAs are typically transcribed with extended 5' and 3' ends that must be removed before they attain their active form. One of the first steps of tRNA processing in nearly every organism is the removal of the 5' leader sequence by ribonuclease P (RNase P). Here, we investigate a recently discovered class of RNase P enzymes, Homologs of Aquifex RNase P (HARPs). In contrast to other RNase Ps, HARPs consist only of a metallonuclease domain and lack the canonical substrate recognition domain essential in other classes of proteinaceous RNase P. We determined the cryo-EM structure of Aquifex aeolicus HARP (Aq880) and two crystal structures of Hydrogenobacter thermophilus HARP (Hth1307) to reveal that both enzymes form large ring-like assemblies: a dodecamer in Aq880 and a tetradecamer in Hth1307. In both oligomers, the enzyme active site is 42 Å away from a positively charged helical region, as seen in other protein-only RNase P enzymes, which likely serves to recognize and bind the elbow region of the pre-tRNA substrate. In addition, we use native mass spectrometry to confirm and characterize the previously unreported tetradecamer state. Notably, we find that multiple oligomeric states of Hth1307 are able to cleave pre-tRNAs. Furthermore, our single-turnover kinetic studies indicate that Hth1307 cleaves pre-tRNAs from multiple species with a preference for native substrates. These data provide a closer look at the nuanced similarities and differences in tRNA processing across disparate classes of RNase P.
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Affiliation(s)
| | - Leena Mallik
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Center for Computational and Genomic Medicine and Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Abigail L Kelly
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Shayna Brotzman
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Johnny Mendoza
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Anna G Anders
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Suada Leskaj
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Carmen Castillo
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A Cianfrocco
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA; Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA.
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13
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Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Đorđević-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.548955. [PMID: 37503021 PMCID: PMC10369999 DOI: 10.1101/2023.07.14.548955] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Structural biology efforts using cryogenic electron microscopy are frequently stifled by specimens adopting "preferred orientations" on grids, leading to anisotropic map resolution and impeding structure determination. Tilting the specimen stage during data collection is a generalizable solution but has historically led to substantial resolution attenuation. Here, we develop updated data collection and image processing workflows and demonstrate, using multiple specimens, that resolution attenuation is negligible or significantly reduced across tilt angles. Reconstructions with and without the stage tilted as high as 60° are virtually indistinguishable. These strategies allowed the reconstruction to 3 Å resolution of a bacterial RNA polymerase with preferred orientation. Furthermore, we present a quantitative framework that allows cryo-EM practitioners to define an optimal tilt angle for dataset acquisition. These data reinforce the utility of employing stage tilt for data collection and provide quantitative metrics to obtain isotropic maps.
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14
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Bryer AJ, Rey JS, Perilla JR. Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining. Nat Commun 2023; 14:2014. [PMID: 37037809 PMCID: PMC10086035 DOI: 10.1038/s41467-023-37801-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 03/30/2023] [Indexed: 04/12/2023] Open
Abstract
Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine.
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Affiliation(s)
- Alexander J Bryer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Juan S Rey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
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15
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Shi H, Wu C, Zhang X. Addressing compressive deformation of proteins embedded in crystalline ice. Structure 2023; 31:213-220.e3. [PMID: 36586403 DOI: 10.1016/j.str.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 08/09/2022] [Accepted: 11/29/2022] [Indexed: 12/31/2022]
Abstract
For cryoelectron microscopy (cryo-EM), high cooling rates have been required for preparation of protein samples to vitrify the surrounding water and avoid formation of damaging crystalline ice. Whether and how crystalline ice affects single-particle cryo-EM is still unclear. Here, single-particle cryo-EM was used to analyze three-dimensional structures of various proteins and viruses embedded in crystalline ice formed at various cooling rates. Low cooling rates led to shrinkage deformation and density distortions on samples having loose structures. Higher cooling rates reduced deformations. Deformation-free proteins in crystalline ice were obtained by modifying the freezing conditions, and reconstructions from these samples revealed a marked improvement over vitreous ice. This procedure also increased the efficiency of cryo-EM structure determinations and was essential for high-resolution reconstructions.
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Affiliation(s)
- Huigang Shi
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Chunling Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing 100101, P.R. China; University of Chinese Academy of Sciences, Beijing 100049, P.R. China.
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16
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Sarewicz M, Szwalec M, Pintscher S, Indyka P, Rawski M, Pietras R, Mielecki B, Koziej Ł, Jaciuk M, Glatt S, Osyczka A. High-resolution cryo-EM structures of plant cytochrome b 6f at work. SCIENCE ADVANCES 2023; 9:eadd9688. [PMID: 36638176 PMCID: PMC9839326 DOI: 10.1126/sciadv.add9688] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
Plants use solar energy to power cellular metabolism. The oxidation of plastoquinol and reduction of plastocyanin by cytochrome b6f (Cyt b6f) is known as one of the key steps of photosynthesis, but the catalytic mechanism in the plastoquinone oxidation site (Qp) remains elusive. Here, we describe two high-resolution cryo-EM structures of the spinach Cyt b6f homodimer with endogenous plastoquinones and in complex with plastocyanin. Three plastoquinones are visible and line up one after another head to tail near Qp in both monomers, indicating the existence of a channel in each monomer. Therefore, quinones appear to flow through Cyt b6f in one direction, transiently exposing the redox-active ring of quinone during catalysis. Our work proposes an unprecedented one-way traffic model that explains efficient quinol oxidation during photosynthesis and respiration.
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Affiliation(s)
- Marcin Sarewicz
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Mateusz Szwalec
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Sebastian Pintscher
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
| | - Paulina Indyka
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
- National Synchrotron Radiation Centre SOLARIS, Jagiellonian University, Kraków, Poland
| | - Michał Rawski
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
| | - Rafał Pietras
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Bohun Mielecki
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Łukasz Koziej
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
| | - Marcin Jaciuk
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
| | - Sebastian Glatt
- Małopolska Centre of Biotechnology (MCB), Jagiellonian University, Kraków, Poland
| | - Artur Osyczka
- Faculty of Biochemistry, Biophysics, and Biotechnology, Jagiellonian University, Kraków, Poland
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17
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Peng R, Fu X, Mendez JH, Randolph PS, Bammes BE, Stagg SM. Characterizing the resolution and throughput of the Apollo direct electron detector. J Struct Biol X 2022; 7:100080. [PMID: 36578473 PMCID: PMC9791170 DOI: 10.1016/j.yjsbx.2022.100080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Advances in electron detection have been essential to the success of high-resolution cryo-EM structure determination. A new generation of direct electron detector called the Apollo, has been developed by Direct Electron. The Apollo uses a novel event-based MAPS detector custom designed for ultra-fast electron counting. We have evaluated this new camera, finding that it delivers high detective quantum efficiency (DQE) and low coincidence loss, enabling high-quality electron counting data acquisition at up to nearly 80 input electrons per pixel per second. We further characterized the performance of Apollo for single particle cryo-EM on real biological samples. Using mouse apoferritin, Apollo yielded better than 1.9 Å resolution reconstructions at all three tested dose rates from a half-day data collection session each. With longer collection time and improved specimen preparation, mouse apoferritin was reconstructed to 1.66 Å resolution. Applied to a more challenging small protein aldolase, we obtained a 2.24 Å resolution reconstruction. The high quality of the map indicates that the Apollo has sufficiently high DQE to reconstruct smaller proteins and complexes with high-fidelity. Our results demonstrate that the Apollo camera performs well across a broad range of dose rates and is capable of capturing high quality data that produce high-resolution reconstructions for large and small single particle samples.
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Affiliation(s)
- Ruizhi Peng
- Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States
| | - Xiaofeng Fu
- Department of Biological Sciences, 319 Stadium Drive, Tallahassee, FL 32306, United States
| | - Joshua H. Mendez
- Simons Electron Microscopy Center, 89 Convent Avenue, New York, NY 10027, United States
| | - Peter S. Randolph
- Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States
| | - Benjamin E. Bammes
- Direct Electron LP, 13240 Evening Creek Drive South, Suite 311, San Diego, CA 92128, United States
| | - Scott M. Stagg
- Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States,Department of Biological Sciences, 319 Stadium Drive, Tallahassee, FL 32306, United States,Corresponding author at: Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States
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18
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Hutin S, Ling WL, Tarbouriech N, Schoehn G, Grimm C, Fischer U, Burmeister WP. The Vaccinia Virus DNA Helicase Structure from Combined Single-Particle Cryo-Electron Microscopy and AlphaFold2 Prediction. Viruses 2022; 14:2206. [PMID: 36298761 PMCID: PMC9611036 DOI: 10.3390/v14102206] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
Poxviruses are large DNA viruses with a linear double-stranded DNA genome circularized at the extremities. The helicase-primase D5, composed of six identical 90 kDa subunits, is required for DNA replication. D5 consists of a primase fragment flexibly attached to the hexameric C-terminal polypeptide (res. 323-785) with confirmed nucleotide hydrolase and DNA-binding activity but an elusive helicase activity. We determined its structure by single-particle cryo-electron microscopy. It displays an AAA+ helicase core flanked by N- and C-terminal domains. Model building was greatly helped by the predicted structure of D5 using AlphaFold2. The 3.9 Å structure of the N-terminal domain forms a well-defined tight ring while the resolution decreases towards the C-terminus, still allowing the fit of the predicted structure. The N-terminal domain is partially present in papillomavirus E1 and polyomavirus LTA helicases, as well as in a bacteriophage NrS-1 helicase domain, which is also closely related to the AAA+ helicase domain of D5. Using the Pfam domain database, a D5_N domain followed by DUF5906 and Pox_D5 domains could be assigned to the cryo-EM structure, providing the first 3D structures for D5_N and Pox_D5 domains. The same domain organization has been identified in a family of putative helicases from large DNA viruses, bacteriophages, and selfish DNA elements.
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Affiliation(s)
- Stephanie Hutin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes (UGA), Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
| | - Wai Li Ling
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes (UGA), Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
| | - Nicolas Tarbouriech
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes (UGA), Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
| | - Guy Schoehn
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes (UGA), Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
| | - Clemens Grimm
- Biozentrum, University of Würzburg, 97070 Würzburg, Germany
| | - Utz Fischer
- Biozentrum, University of Würzburg, 97070 Würzburg, Germany
| | - Wim P. Burmeister
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes (UGA), Commissariat à l’Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), 38000 Grenoble, France
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19
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Abstract
Cryo-electron microscopy (CryoEM) has become a vital technique in structural biology. It is an interdisciplinary field that takes advantage of advances in biochemistry, physics, and image processing, among other disciplines. Innovations in these three basic pillars have contributed to the boosting of CryoEM in the past decade. This work reviews the main contributions in image processing to the current reconstruction workflow of single particle analysis (SPA) by CryoEM. Our review emphasizes the time evolution of the algorithms across the different steps of the workflow differentiating between two groups of approaches: analytical methods and deep learning algorithms. We present an analysis of the current state of the art. Finally, we discuss the emerging problems and challenges still to be addressed in the evolution of CryoEM image processing methods in SPA.
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Affiliation(s)
- Jose Luis Vilas
- Biocomputing Unit, Centro
Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Jose Maria Carazo
- Biocomputing Unit, Centro
Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
| | - Carlos Oscar S. Sorzano
- Biocomputing Unit, Centro
Nacional de Biotecnologia (CNB-CSIC), Darwin, 3, Campus Universidad Autonoma, 28049 Cantoblanco, Madrid, Spain
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20
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Melville Z, Dridi H, Yuan Q, Reiken S, Wronska A, Liu Y, Clarke OB, Marks AR. A drug and ATP binding site in type 1 ryanodine receptor. Structure 2022; 30:1025-1034.e4. [PMID: 35580609 DOI: 10.1016/j.str.2022.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/02/2022] [Accepted: 04/21/2022] [Indexed: 12/12/2022]
Abstract
The ryanodine receptor (RyR)/calcium release channel on the sarcoplasmic reticulum (SR) is required for excitation-contraction coupling in skeletal and cardiac muscle. Inherited mutations and stress-induced post-translational modifications result in an SR Ca2+ leak that causes skeletal myopathies, heart failure, and exercise-induced sudden death. A class of therapeutics known as Rycals prevent the RyR-mediated leak, are effective in preventing disease progression and restoring function in animal models, and are in clinical trials for patients with muscle and heart disorders. Using cryogenic-electron microscopy, we present a model of RyR1 with a 2.45-Å resolution before local refinement, revealing a binding site in the RY1&2 domain (3.10 Å local resolution), where the Rycal ARM210 binds cooperatively with ATP and stabilizes the closed state of RyR1.
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Affiliation(s)
- Zephan Melville
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Haikel Dridi
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Qi Yuan
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Steven Reiken
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Anetta Wronska
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Yang Liu
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA; Department of Anesthesiology, Columbia University, New York, NY, USA
| | - Andrew R Marks
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA; Clyde & Helen Wu Center for Molecular Cardiology, Columbia University, New York, NY, USA.
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21
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Gomez-Blanco J, Kaur S, Strauss M, Vargas J. Hierarchical autoclassification of cryo-EM samples and macromolecular energy landscape determination. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 216:106673. [PMID: 35149430 DOI: 10.1016/j.cmpb.2022.106673] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/10/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND OBJECTIVE Cryo-electron microscopy using single particle analysis is a powerful technique for obtaining 3D reconstructions of macromolecules in near native conditions. One of its major advances is its capacity to reveal conformations of dynamic molecular complexes. Most popular and successful current approaches to analyzing heterogeneous complexes are founded on Bayesian inference. However, these 3D classification methods require the tuning of specific parameters by the user and the use of complicated 3D re-classification procedures for samples affected by extensive heterogeneity. Thus, the success of these approaches highly depends on the user experience. We introduce a robust approach to identify many different conformations presented in a cryo-EM dataset based on Bayesian inference through Relion classification methods that does not require tuning of parameters and reclassification strategies. METHODS The algorithm allows both 2D and 3D classification and is based on a hierarchical clustering approach that runs automatically without requiring typical inputs, such as the number of conformations present in the dataset or the required classification iterations. This approach is applied to robustly determine the energy landscapes of macromolecules. RESULTS We tested the performance of the methods proposed here using four different datasets, comprising structurally homogeneous and highly heterogeneous cases. In all cases, the approach provided excellent results. The routines are publicly available as part of the CryoMethods plugin included in the Scipion package. CONCLUSIONS Our results show that the proposed method can be used to align and classify homogeneous and heterogeneous datasets without requiring previous alignment information or any prior knowledge about the number of co-existing conformations. The approach can be used for both 2D and 3D autoclassification and only requires an initial volume. In addition, the approach is robust to the "attractor" problem providing many different conformations/views for samples affected by extensive heterogeneity. The obtained 3D classes can render high resolution 3D structures, while the obtained energy landscapes can be used to determine structural trajectories.
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Affiliation(s)
- J Gomez-Blanco
- Departamento de Óptica, Universidad Complutense de Madrid, Plaza de Ciencias 1, 28040, Spain
| | - S Kaur
- Department of Anatomy and Cell Biology, McGill University, 3640 Rue University, Montréal, QC H3A 0C7, Canada
| | - M Strauss
- Department of Anatomy and Cell Biology, McGill University, 3640 Rue University, Montréal, QC H3A 0C7, Canada
| | - J Vargas
- Departamento de Óptica, Universidad Complutense de Madrid, Plaza de Ciencias 1, 28040, Spain.
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22
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Huber ST, Sarajlic E, Huijink R, Weis F, Evers WH, Jakobi AJ. Nanofluidic chips for cryo-EM structure determination from picoliter sample volumes. eLife 2022; 11:72629. [PMID: 35060902 PMCID: PMC8786315 DOI: 10.7554/elife.72629] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/07/2021] [Indexed: 01/25/2023] Open
Abstract
Cryogenic electron microscopy has become an essential tool for structure determination of biological macromolecules. In practice, the difficulty to reliably prepare samples with uniform ice thickness still represents a barrier for routine high-resolution imaging and limits the current throughput of the technique. We show that a nanofluidic sample support with well-defined geometry can be used to prepare cryo-EM specimens with reproducible ice thickness from picoliter sample volumes. The sample solution is contained in electron-transparent nanochannels that provide uniform thickness gradients without further optimisation and eliminate the potentially destructive air-water interface. We demonstrate the possibility to perform high-resolution structure determination with three standard protein specimens. Nanofabricated sample supports bear potential to automate the cryo-EM workflow, and to explore new frontiers for cryo-EM applications such as time-resolved imaging and high-throughput screening.
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Affiliation(s)
- Stefan T Huber
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology
| | | | | | - Felix Weis
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL)
| | - Wiel H Evers
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology
| | - Arjen J Jakobi
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology
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23
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Melville Z, Kim K, Clarke OB, Marks AR. High-resolution structure of the membrane-embedded skeletal muscle ryanodine receptor. Structure 2022; 30:172-180.e3. [PMID: 34469755 PMCID: PMC8741649 DOI: 10.1016/j.str.2021.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/23/2021] [Accepted: 08/10/2021] [Indexed: 12/17/2022]
Abstract
The type 1 ryanodine receptor (RyR)/calcium release channel on the sarcoplasmic reticulum (SR) is required for skeletal muscle excitation-contraction coupling and is the largest known ion channel, composed of four 565-kDa protomers. Cryogenic electron microscopy (cryo-EM) studies of the RyR have primarily used detergent to solubilize the channel; in the present study, we have used cryo-EM to solve high-resolution structures of the channel in liposomes using a gel-filtration approach with on-column detergent removal to form liposomes and incorporate the channel simultaneously. This allowed us to resolve the structure of the channel in the primed and open states at 3.4 and 4.0 Å, respectively, with a single dataset. This method offers validation for detergent-based structures of the RyR and offers a starting point for utilizing a chemical gradient mimicking the SR, where Ca2+ concentrations are millimolar in the lumen and nanomolar in the cytosol.
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Affiliation(s)
- Zephan Melville
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA
| | - Kookjoo Kim
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA
| | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA; Department of Anesthesiology, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA
| | - Andrew R Marks
- Department of Physiology and Cellular Biophysics, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA; Clyde & Helen Wu Center for Molecular Cardiology, Columbia University Vagelos College of Physicians & Surgeons, New York, NY, USA.
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24
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Low-cooling-rate freezing in biomolecular cryo-electron microscopy for recovery of initial frames. QRB DISCOVERY 2021. [PMID: 37529673 PMCID: PMC10392635 DOI: 10.1017/qrd.2021.8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abstract
When biological samples are first exposed to electrons in cryo-electron microcopy (cryo-EM), proteins exhibit a rapid ‘burst’ phase of beam-induced motion that cannot be corrected with software. This lowers the quality of the initial frames, which are the least damaged by the electrons. Hence, they are commonly excluded or down-weighted during data processing, reducing the undamaged signal and the resolution in the reconstruction. By decreasing the cooling rate during sample preparation, either with a cooling-rate gradient or by increasing the freezing temperature, we show that the quality of the initial frames for various protein and virus samples can be recovered. Incorporation of the initial frames in the reconstruction increases the resolution by an amount equivalent to using ~60% more data. Moreover, these frames preserve the high-quality cryo-EM densities of radiation-sensitive residues, which is often damaged or very weak in canonical three-dimensional reconstruction. The improved freezing conditions can be easily achieved using existing devices and enhance the overall quality of cryo-EM structures.
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25
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Sorzano COS, Jiménez-Moreno A, Maluenda D, Ramírez-Aportela E, Martínez M, Cuervo A, Melero R, Conesa JJ, Sánchez-García R, Strelak D, Filipovic J, Fernández-Giménez E, de Isidro-Gómez F, Herreros D, Conesa P, Del Caño L, Fonseca Y, de la Morena JJ, Macías JR, Losana P, Marabini R, Carazo JM. Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods. Methods Mol Biol 2021; 2305:257-289. [PMID: 33950394 DOI: 10.1007/978-1-0716-1406-8_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cryo-electron microscopy has established as a mature structural biology technique to elucidate the three-dimensional structure of biological macromolecules. The Coulomb potential of the sample is imaged by an electron beam, and fast semi-conductor detectors produce movies of the sample under study. These movies have to be further processed by a whole pipeline of image-processing algorithms that produce the final structure of the macromolecule. In this chapter, we illustrate this whole processing pipeline putting in value the strength of "meta algorithms," which are the combination of several algorithms, each one with different mathematical rationale, in order to distinguish correctly from incorrectly estimated parameters. We show how this strategy leads to superior performance of the whole pipeline as well as more confident assessments about the reconstructed structures. The "meta algorithms" strategy is common to many fields and, in particular, it has provided excellent results in bioinformatics. We illustrate this combination using the workflow engine, Scipion.
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Affiliation(s)
| | | | | | | | | | - Ana Cuervo
- National Centre for Biotechnology (CSIC), Madrid, Spain
| | - Robert Melero
- National Centre for Biotechnology (CSIC), Madrid, Spain
| | | | | | - David Strelak
- National Centre for Biotechnology (CSIC), Madrid, Spain
| | | | | | | | | | - Pablo Conesa
- National Centre for Biotechnology (CSIC), Madrid, Spain
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26
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Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs. Nat Struct Mol Biol 2021; 28:573-582. [PMID: 34158638 PMCID: PMC8772433 DOI: 10.1038/s41594-021-00619-0] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 ORF3a is a putative viral ion channel implicated in autophagy inhibition, inflammasome activation and apoptosis. 3a protein and anti-3a antibodies are found in infected patient tissues and plasma. Deletion of 3a in SARS-CoV-1 reduces viral titer and morbidity in mice, suggesting it could be an effective target for vaccines or therapeutics. Here, we present structures of SARS-CoV-2 3a determined by cryo-EM to 2.1-Å resolution. 3a adopts a new fold with a polar cavity that opens to the cytosol and membrane through separate water- and lipid-filled openings. Hydrophilic grooves along outer helices could form ion-conduction paths. Using electrophysiology and fluorescent ion imaging of 3a-reconstituted liposomes, we observe Ca2+-permeable, nonselective cation channel activity, identify mutations that alter ion permeability and discover polycationic inhibitors of 3a activity. 3a-like proteins are found across coronavirus lineages that infect bats and humans, suggesting that 3a-targeted approaches could treat COVID-19 and other coronavirus diseases.
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27
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Kern DM, Sorum B, Mali SS, Hoel CM, Sridharan S, Remis JP, Toso DB, Kotecha A, Bautista DM, Brohawn SG. Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 32587976 PMCID: PMC7310636 DOI: 10.1101/2020.06.17.156554] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes the coronavirus disease 2019 (COVID-19). SARS-CoV-2 encodes three putative ion channels: E, 8a, and 3a1,2. 3a is expressed in SARS patient tissue and anti-3a antibodies are observed in patient plasma3–6. 3a has been implicated in viral release7, inhibition of autophagy8, inflammasome activation9, and cell death10,11 and its deletion reduces viral titer and morbidity in mice1, raising the possibility that 3a could be an effective vaccine or therapeutic target3,12. Here, we present the first cryo-EM structures of SARS-CoV-2 3a to 2.1 Å resolution and demonstrate 3a forms an ion channel in reconstituted liposomes. The structures in lipid nanodiscs reveal 3a dimers and tetramers adopt a novel fold with a large polar cavity that spans halfway across the membrane and is accessible to the cytosol and the surrounding bilayer through separate water- and lipid-filled openings. Electrophysiology and fluorescent ion imaging experiments show 3a forms Ca2+-permeable non-selective cation channels. We identify point mutations that alter ion permeability and discover polycationic inhibitors of 3a channel activity. We find 3a-like proteins in multiple Alphacoronavirus and Betacoronavirus lineages that infect bats and humans. These data show 3a forms a functional ion channel that may promote COVID-19 pathogenesis and suggest targeting 3a could broadly treat coronavirus diseases.
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Affiliation(s)
- David M Kern
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720
| | - Ben Sorum
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720
| | - Sonali S Mali
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Christopher M Hoel
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720
| | - Savitha Sridharan
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Jonathan P Remis
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720
| | - Daniel B Toso
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, The Netherlands
| | - Diana M Bautista
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA
| | - Stephen G Brohawn
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California 94720, USA.,Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, California 94720, USA.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720
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28
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Kazemi M, Sorzano COS, Carazo JM, Georges AD, Abrishami V, Vargas J. ENRICH: A fast method to improve the quality of flexible macromolecular reconstructions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 164:92-100. [PMID: 33450244 DOI: 10.1016/j.pbiomolbio.2021.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 11/27/2022]
Abstract
Cryo-electron microscopy using single particle analysis requires the computational averaging of thousands of projection images captured from identical macromolecules. However, macromolecules usually present some degree of flexibility showing different conformations. Computational approaches are then required to classify heterogeneous single particle images into homogeneous sets corresponding to different structural states. Nonetheless, sometimes the attainable resolution of reconstructions obtained from these smaller homogeneous sets is compromised because of reduced number of particles or lack of images at certain macromolecular orientations. In these situations, the current solution to improve map resolution is returning to the electron microscope and collect more data. In this work, we present a fast approach to partially overcome this limitation for heterogeneous data sets. Our method is based on deforming and then moving particles between different conformations using an optical flow approach. Particles are then merged into a unique conformation obtaining reconstructions with improved resolution, contrast and signal-to-noise ratio. We present experimental results that show clear improvements in the quality of obtained 3D maps, however, there are also limits to this approach, i.e., the method is restricted to small deformations and cannot determine local patterns of flexibility of small elements, such as secondary structures, which we discuss in the manuscript.
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Affiliation(s)
- M Kazemi
- Dep. of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049, Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049, Cantoblanco, Madrid, Spain
| | - A des Georges
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA; Dept. of Chemistry & Biochemistry, City College of New York, New York, NY, 10031, USA; Ph.D. Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - V Abrishami
- Laboratory of Structural Biology, Helsinki Institute of Life Science HiLIFE, Finland
| | - J Vargas
- Departamento de Optica, Universidad Complutense de Madrid, Avda. Computense s/n, Ciudad Universitaria, 28040, Madrid, Spain; Department of Anatomy and Cell Biology, McGill University, 3640, Rue University, Montréal, QC, H3A 0C7, Canada.
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29
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Yan R, Cao P, Song W, Qian H, Du X, Coates HW, Zhao X, Li Y, Gao S, Gong X, Liu X, Sui J, Lei J, Yang H, Brown AJ, Zhou Q, Yan C, Yan N. A structure of human Scap bound to Insig-2 suggests how their interaction is regulated by sterols. Science 2021; 371:science.abb2224. [PMID: 33446483 DOI: 10.1126/science.abb2224] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 07/31/2020] [Accepted: 01/06/2021] [Indexed: 12/22/2022]
Abstract
The sterol regulatory element-binding protein (SREBP) pathway controls cellular homeostasis of sterols. The key players in this pathway, Scap and Insig-1 and -2, are membrane-embedded sterol sensors. The 25-hydroxycholesterol (25HC)-dependent association of Scap and Insig acts as the master switch for the SREBP pathway. Here, we present cryo-electron microscopy analysis of the human Scap and Insig-2 complex in the presence of 25HC, with the transmembrane (TM) domains determined at an average resolution of 3.7 angstrom. The sterol-sensing domain in Scap and all six TMs in Insig-2 were resolved. A 25HC molecule is sandwiched between the S4 to S6 segments in Scap and TMs 3 and 4 in Insig-2 in the luminal leaflet of the membrane. Unwinding of the middle of the Scap-S4 segment is crucial for 25HC binding and Insig association.
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Affiliation(s)
- Renhong Yan
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Pingping Cao
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenqi Song
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongwu Qian
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Ximing Du
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Hudson W Coates
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Xin Zhao
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yaning Li
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shuai Gao
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Xin Gong
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Ximing Liu
- National Institute of Biological Sciences (NIBS), Beijing 102206, China
| | - Jianhua Sui
- National Institute of Biological Sciences (NIBS), Beijing 102206, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Jianlin Lei
- Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hongyuan Yang
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Andrew J Brown
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, NSW 2052, Australia
| | - Qiang Zhou
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, Hangzhou 310024, Zhejiang Province, China
| | - Chuangye Yan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
| | - Nieng Yan
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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30
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Higher-order phosphatase-substrate contacts terminate the integrated stress response. Nat Struct Mol Biol 2021; 28:835-846. [PMID: 34625748 PMCID: PMC8500838 DOI: 10.1038/s41594-021-00666-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/23/2021] [Indexed: 01/09/2023]
Abstract
Many regulatory PPP1R subunits join few catalytic PP1c subunits to mediate phosphoserine and phosphothreonine dephosphorylation in metazoans. Regulatory subunits engage the surface of PP1c, locally affecting flexible access of the phosphopeptide to the active site. However, catalytic efficiency of holophosphatases towards their phosphoprotein substrates remains unexplained. Here we present a cryo-EM structure of the tripartite PP1c-PPP1R15A-G-actin holophosphatase that terminates signaling in the mammalian integrated stress response (ISR) in the pre-dephosphorylation complex with its substrate, translation initiation factor 2α (eIF2α). G-actin, whose essential role in eIF2α dephosphorylation is supported crystallographically, biochemically and genetically, aligns the catalytic and regulatory subunits, creating a composite surface that engages the N-terminal domain of eIF2α to position the distant phosphoserine-51 at the active site. Substrate residues that mediate affinity for the holophosphatase also make critical contacts with eIF2α kinases. Thus, a convergent process of higher-order substrate recognition specifies functionally antagonistic phosphorylation and dephosphorylation in the ISR.
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31
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Punjani A, Zhang H, Fleet DJ. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat Methods 2020; 17:1214-1221. [PMID: 33257830 DOI: 10.1038/s41592-020-00990-8] [Citation(s) in RCA: 704] [Impact Index Per Article: 176.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 10/06/2020] [Indexed: 11/09/2022]
Abstract
Cryogenic electron microscopy (cryo-EM) is widely used to study biological macromolecules that comprise regions with disorder, flexibility or partial occupancy. For example, membrane proteins are often kept in solution with detergent micelles and lipid nanodiscs that are locally disordered. Such spatial variability negatively impacts computational three-dimensional (3D) reconstruction with existing iterative refinement algorithms that assume rigidity. We introduce non-uniform refinement, an algorithm based on cross-validation optimization, which automatically regularizes 3D density maps during refinement to account for spatial variability. Unlike common shift-invariant regularizers, non-uniform refinement systematically removes noise from disordered regions, while retaining signal useful for aligning particle images, yielding dramatically improved resolution and 3D map quality in many cases. We obtain high-resolution reconstructions for multiple membrane proteins as small as 100 kDa, demonstrating increased effectiveness of cryo-EM for this class of targets critical in structural biology and drug discovery. Non-uniform refinement is implemented in the cryoSPARC software package.
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Affiliation(s)
- Ali Punjani
- Department of Computer Sciences, University of Toronto, Toronto, Ontario, Canada. .,Vector Institute, Toronto, Ontario, Canada. .,Structura Biotechnology Inc., Toronto, Ontario, Canada.
| | - Haowei Zhang
- Department of Computer Sciences, University of Toronto, Toronto, Ontario, Canada
| | - David J Fleet
- Department of Computer Sciences, University of Toronto, Toronto, Ontario, Canada. .,Vector Institute, Toronto, Ontario, Canada.
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32
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Miller-Vedam LE, Bräuning B, Popova KD, Schirle Oakdale NT, Bonnar JL, Prabu JR, Boydston EA, Sevillano N, Shurtleff MJ, Stroud RM, Craik CS, Schulman BA, Frost A, Weissman JS. Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. eLife 2020; 9:e62611. [PMID: 33236988 PMCID: PMC7785296 DOI: 10.7554/elife.62611] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Membrane protein biogenesis in the endoplasmic reticulum (ER) is complex and failure-prone. The ER membrane protein complex (EMC), comprising eight conserved subunits, has emerged as a central player in this process. Yet, we have limited understanding of how EMC enables insertion and integrity of diverse clients, from tail-anchored to polytopic transmembrane proteins. Here, yeast and human EMC cryo-EM structures reveal conserved intricate assemblies and human-specific features associated with pathologies. Structure-based functional studies distinguish between two separable EMC activities, as an insertase regulating tail-anchored protein levels and a broader role in polytopic membrane protein biogenesis. These depend on mechanistically coupled yet spatially distinct regions including two lipid-accessible membrane cavities which confer client-specific regulation, and a non-insertase EMC function mediated by the EMC lumenal domain. Our studies illuminate the structural and mechanistic basis of EMC's multifunctionality and point to its role in differentially regulating the biogenesis of distinct client protein classes.
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Affiliation(s)
- Lakshmi E Miller-Vedam
- Molecular, Cellular, and Computational Biophysics Graduate Program, University of California, San FranciscoSan FranciscoUnited States
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Bastian Bräuning
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Katerina D Popova
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Biomedical Sciences Graduate Program, University of California, San FranciscoSan FranciscoUnited States
| | - Nicole T Schirle Oakdale
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Jessica L Bonnar
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Jesuraj R Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Elizabeth A Boydston
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Natalia Sevillano
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Matthew J Shurtleff
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San FranciscoSan FranciscoUnited States
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of BiochemistryMartinsriedGermany
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San FranciscoSan FranciscoUnited States
| | - Jonathan S Weissman
- Department of Biology, Whitehead Institute, MITCambridgeUnited States
- Department of Cellular and Molecular Pharmacology, University of California, San FranciscoSan FranciscoUnited States
- Howard Hughes Medical InstituteChevy ChaseUnited States
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Palovcak E, Asarnow D, Campbell MG, Yu Z, Cheng Y. Enhancing the signal-to-noise ratio and generating contrast for cryo-EM images with convolutional neural networks. IUCRJ 2020; 7:1142-1150. [PMID: 33209325 PMCID: PMC7642784 DOI: 10.1107/s2052252520013184] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/29/2020] [Indexed: 05/10/2023]
Abstract
In cryogenic electron microscopy (cryo-EM) of radiation-sensitive biological samples, both the signal-to-noise ratio (SNR) and the contrast of images are critically important in the image-processing pipeline. Classic methods improve low-frequency image contrast experimentally, by imaging with high defocus, or computationally, by applying various types of low-pass filter. These contrast improvements typically come at the expense of the high-frequency SNR, which is suppressed by high-defocus imaging and removed by low-pass filtration. Recently, convolutional neural networks (CNNs) trained to denoise cryo-EM images have produced impressive gains in image contrast, but it is not clear how these algorithms affect the information content of the image. Here, a denoising CNN for cryo-EM images was implemented and a quantitative evaluation of SNR enhancement, induced bias and the effects of denoising on image processing and three-dimensional reconstructions was performed. The study suggests that besides improving the visual contrast of cryo-EM images, the enhanced SNR of denoised images may be used in other parts of the image-processing pipeline, such as classification and 3D alignment. These results lay the groundwork for the use of denoising CNNs in the cryo-EM image-processing pipeline beyond particle picking.
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Affiliation(s)
- Eugene Palovcak
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Daniel Asarnow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Melody G. Campbell
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Zanlin Yu
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94143, USA
- Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94132, USA
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Xie Q, Yoshioka CK, Chapman MS. Adeno-Associated Virus (AAV-DJ)-Cryo-EM Structure at 1.56 Å Resolution. Viruses 2020; 12:E1194. [PMID: 33092282 PMCID: PMC7589773 DOI: 10.3390/v12101194] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 01/12/2023] Open
Abstract
Adeno-associated virus is the leading viral vector for gene therapy. AAV-DJ is a recombinant variant developed for tropism to the liver. The AAV-DJ structure has been determined to 1.56 Å resolution through cryo-electron microscopy (cryo-EM). Only apoferritin is reported in preprints at 1.6 Å or higher resolution, and AAV-DJ nearly matches the highest resolutions ever attained through X-ray diffraction of virus crystals. However, cryo-EM has the advantage that most of the hydrogens are clear, improving the accuracy of atomic refinement, and removing ambiguity in hydrogen bond identification. Outside of secondary structures where hydrogen bonding was predictable a priori, the networks of hydrogen bonds coming from direct observation of hydrogens and acceptor atoms are quite different from those inferred even at 2.8 Å resolution. The implications for understanding viral assembly mean that cryo-EM will likely become the favored approach for high resolution structural virology.
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Affiliation(s)
- Qing Xie
- Department of Biochemistry & Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Craig K. Yoshioka
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA;
| | - Michael S. Chapman
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
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Bepler T, Kelley K, Noble AJ, Berger B. Topaz-Denoise: general deep denoising models for cryoEM and cryoET. Nat Commun 2020; 11:5208. [PMID: 33060581 PMCID: PMC7567117 DOI: 10.1038/s41467-020-18952-1] [Citation(s) in RCA: 208] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 09/14/2020] [Indexed: 01/21/2023] Open
Abstract
Cryo-electron microscopy (cryoEM) is becoming the preferred method for resolving protein structures. Low signal-to-noise ratio (SNR) in cryoEM images reduces the confidence and throughput of structure determination during several steps of data processing, resulting in impediments such as missing particle orientations. Denoising cryoEM images can not only improve downstream analysis but also accelerate the time-consuming data collection process by allowing lower electron dose micrographs to be used for analysis. Here, we present Topaz-Denoise, a deep learning method for reliably and rapidly increasing the SNR of cryoEM images and cryoET tomograms. By training on a dataset composed of thousands of micrographs collected across a wide range of imaging conditions, we are able to learn models capturing the complexity of the cryoEM image formation process. The general model we present is able to denoise new datasets without additional training. Denoising with this model improves micrograph interpretability and allows us to solve 3D single particle structures of clustered protocadherin, an elongated particle with previously elusive views. We then show that low dose collection, enabled by Topaz-Denoise, improves downstream analysis in addition to reducing data collection time. We also present a general 3D denoising model for cryoET. Topaz-Denoise and pre-trained general models are now included in Topaz. We expect that Topaz-Denoise will be of broad utility to the cryoEM community for improving micrograph and tomogram interpretability and accelerating analysis.
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Affiliation(s)
- Tristan Bepler
- Computational and Systems Biology, MIT, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - Kotaro Kelley
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Alex J Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.
- Department of Mathematics, MIT, Cambridge, MA, USA.
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36
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Merk A, Fukumura T, Zhu X, Darling JE, Grisshammer R, Ognjenovic J, Subramaniam S. 1.8 Å resolution structure of β-galactosidase with a 200 kV CRYO ARM electron microscope. IUCRJ 2020; 7:639-643. [PMID: 32695410 PMCID: PMC7340270 DOI: 10.1107/s2052252520006855] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 05/20/2020] [Indexed: 05/26/2023]
Abstract
We report the determination of the structure of Escherichia coli β-galactosidase at a resolution of ∼1.8 Å using data collected on a 200 kV CRYO ARM microscope equipped with a K3 direct electron detector. The data were collected in a single 24 h session by recording images from an array of 7 × 7 holes at each stage position using the automated data collection program SerialEM. In addition to the expected features such as holes in the densities of aromatic residues, the map also shows density bumps corresponding to the locations of hydrogen atoms. The hydrogen densities are useful in assigning absolute orientations for residues such as glutamine or asparagine by removing the uncertainty in the fitting of the amide groups, and are likely to be especially relevant in the context of structure-guided drug design. These findings validate the use of electron microscopes operating at 200 kV for imaging protein complexes at atomic resolution using cryo-EM.
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Affiliation(s)
- Alan Merk
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | | | - Xing Zhu
- University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Joseph E. Darling
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Reinhard Grisshammer
- National Cancer Institute Frederick Office of Scientific Operations, Frederick, MD 21701, USA
| | - Jana Ognjenovic
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
| | - Sriram Subramaniam
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD 21701, USA
- University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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37
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Cianfrocco MA, Kellogg EH. What Could Go Wrong? A Practical Guide to Single-Particle Cryo-EM: From Biochemistry to Atomic Models. J Chem Inf Model 2020; 60:2458-2469. [PMID: 32078321 DOI: 10.1021/acs.jcim.9b01178] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cryo-electron microscopy (cryo-EM) has enjoyed explosive recent growth due to revolutionary advances in hardware and software, resulting in a steady stream of long-awaited, high-resolution structures with unprecedented atomic detail. With this comes an increased number of microscopes, cryo-EM facilities, and scientists eager to leverage the ability to determine protein structures without crystallization. However, numerous pitfalls and considerations beset the path toward high-resolution structures and are not necessarily obvious from literature surveys. Here, we detail the most common misconceptions when initiating a cryo-EM project and common technical hurdles, as well as their solutions, and we conclude with a vision for the future of this exciting field.
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Affiliation(s)
- Michael A Cianfrocco
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Elizabeth H Kellogg
- Department of Molecular Biology and Genetics,Cornell University, Ithaca, New York 14850, United States
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38
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Mendez JH, Mehrani A, Randolph P, Stagg S. Throughput and resolution with a next-generation direct electron detector. IUCRJ 2019; 6:1007-1013. [PMID: 31709056 PMCID: PMC6830211 DOI: 10.1107/s2052252519012661] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/11/2019] [Indexed: 05/26/2023]
Abstract
Direct electron detectors (DEDs) have revolutionized cryo-electron microscopy (cryo-EM) by facilitating the correction of beam-induced motion and radiation damage, and also by providing high-resolution image capture. A new-generation DED, the DE64, has been developed by Direct Electron that has good performance in both integrating and counting modes. The camera has been characterized in both modes in terms of image quality, throughput and resolution of cryo-EM reconstructions. The modulation transfer function, noise power spectrum and detective quantum efficiency (DQE) were determined for both modes, as well as the number of images per unit time. Although the DQE for counting mode was superior to that for integrating mode, the data-collection throughput for this mode was more than ten times slower. Since throughput and resolution are related in single-particle cryo-EM, data for apoferritin were collected and reconstructed using integrating mode, integrating mode in conjunction with a Volta phase plate (VPP) and counting mode. Only the counting-mode data resulted in a better than 3 Å resolution reconstruction with similar numbers of particles, and this increased performance could not be compensated for by the increased throughput of integrating mode or by the increased low-frequency contrast of integrating mode with the VPP. These data show that the superior image quality provided by counting mode is more important for high-resolution cryo-EM reconstructions than the superior throughput of integrating mode.
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Affiliation(s)
- Joshua H. Mendez
- Department of Physics, Florida State University, 77 Chieftan Way, Tallahassee, FL 32306, USA
| | - Atousa Mehrani
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL 32306, USA
| | - Peter Randolph
- Institute of Molecular Biophysics, Florida State University, 91 Chieftain Way, Tallahassee, FL 32306, USA
| | - Scott Stagg
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, FL 32306, USA
- Institute of Molecular Biophysics, Florida State University, 91 Chieftain Way, Tallahassee, FL 32306, USA
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39
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Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat Methods 2019; 16:1153-1160. [PMID: 31591578 PMCID: PMC6858545 DOI: 10.1038/s41592-019-0575-8] [Citation(s) in RCA: 629] [Impact Index Per Article: 125.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 08/14/2019] [Indexed: 12/14/2022]
Abstract
Cryo-electron microscopy is a popular method for protein structure determination. Identifying a sufficient number of particles for analysis can take months of manual effort. Current computational approaches find many false positives and require significant ad hoc post-processing, especially for unusually-shaped particles. To address these shortcomings, we develop Topaz, an efficient and accurate particle picking pipeline using neural networks trained with a general-purpose positive-unlabeled (PU) learning method. This framework enables particle detection models to be trained with few, sparsely labeled particles and no labeled negatives. Topaz retrieves many more real particles than conventional picking methods while maintaining low false positive rates, is capable of picking challenging unusually-shaped proteins (e.g. small, non-globular, and asymmetric), produces more representative particle sets, and does not require post hoc curation. We demonstrate the performance of Topaz on two difficult datasets and three conventional datasets. Topaz is modular, standalone, free, and open source (http://topaz.csail.mit.edu)
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40
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High-quality, high-throughput cryo-electron microscopy data collection via beam tilt and astigmatism-free beam-image shift. J Struct Biol 2019; 208:107396. [PMID: 31562921 DOI: 10.1016/j.jsb.2019.09.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 09/09/2019] [Accepted: 09/24/2019] [Indexed: 11/23/2022]
Abstract
The throughput of cryo-electron microscopy (cryo-EM) can be improved by employing a procedure that collects beam-image shift data. However, this procedure inadvertently induces a beam tilt, thus decreasing the resolution of the reconstruction. Here, we report an automatic calibration procedure for correcting the beam tilt and a large unexpected astigmatism in the beam-image shift data collection. In this procedure, the changes of the beam tilt and the astigmatism against the beam shift are measured and calibrated. The beam tilt and the astigmatism are corrected by changing the setting of the microscope using predicted values from the calibration. Using our corrected beam-image shift data collection, we found that the resolution remained identical as long as the distance of the beam shift was below 10 μm. The image throughput increases by ∼80%, with image quality improving by reducing the residual stage drift, thus benefiting the high resolution cryo-EM structure determination. Such a calibration procedure takes about 3 h and can be applied to different microscopes.
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41
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Non-uniformity of projection distributions attenuates resolution in Cryo-EM. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:160-183. [PMID: 31525386 DOI: 10.1016/j.pbiomolbio.2019.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/02/2019] [Accepted: 09/07/2019] [Indexed: 11/23/2022]
Abstract
Virtually all single-particle cryo-EM experiments currently suffer from specimen adherence to the air-water interface, leading to a non-uniform distribution in the set of projection views. Whereas it is well accepted that uniform projection distributions can lead to high-resolution reconstructions, non-uniform (anisotropic) distributions can negatively affect map quality, elongate structural features, and in some cases, prohibit interpretation altogether. Although some consequences of non-uniform sampling have been described qualitatively, we know little about how sampling quantitatively affects resolution in cryo-EM. Here, we show how inhomogeneity in any projection distribution scheme attenuates the global Fourier Shell Correlation (FSC) in relation to the number of particles and a single geometrical parameter, which we term the sampling compensation factor (SCF). The reciprocal of the SCF is defined as the average over Fourier shells of the reciprocal of the per-particle sampling and normalized to unity for uniform distributions. The SCF therefore ranges from one to zero, with values close to the latter implying large regions of poorly sampled or completely missing data in Fourier space. Using two synthetic test cases, influenza hemagglutinin and human apoferritin, we demonstrate how any amount of sampling inhomogeneity always attenuates the FSC compared to a uniform distribution. We advocate quantitative evaluation of the SCF criterion to approximate the effect of non-uniform sampling on resolution within experimental single-particle cryo-EM reconstructions.
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42
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Capabilities of the Falcon III detector for single-particle structure determination. Ultramicroscopy 2019; 203:145-154. [PMID: 30738626 DOI: 10.1016/j.ultramic.2019.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/10/2019] [Accepted: 01/26/2019] [Indexed: 02/02/2023]
Abstract
Direct electron detectors are an essential asset for the resolution revolution in electron cryo microscopy of biological objects. The direct detectors provide two modes of data acquisition; the counting mode in which single electrons are counted, and the integrating mode in which the signal that arises from the incident electrons is integrated. While counting mode leads to far higher detective quantum efficiency at all spatial frequencies, the integrating mode enables faster data acquisition at higher exposure rates. For optimal throughput at best possible resolution it is important to understand when the better performance in counting mode becomes essential for solving a structure and when the lower detective quantum efficiency in integrating mode can be compensated by increasing the number of particles in the data set. Here, we provide a case study of the Falcon III camera, which has counting mode capability at exposure rates of <0.9 e-/Px² and integrating mode capability at exposure rates above 10 e-/Px². We found that counting mode gives better resolution for medium sized complexes such as the β-galactosidase (465 kDa) (2.2 Å, 97% of Nyquist vs. 2.4 Å, 89% of Nyquist) with data sets of similar size. However, for larger particles such as Hepatitis B virus capsid like particles (4.8 MDa) we did not find any resolution gain in counting mode.
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43
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Heymann JB. Single-particle reconstruction statistics: a diagnostic tool in solving biomolecular structures by cryo-EM. Acta Crystallogr F Struct Biol Commun 2019; 75:33-44. [PMID: 30605123 PMCID: PMC6317460 DOI: 10.1107/s2053230x18017636] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/13/2018] [Indexed: 11/10/2022] Open
Abstract
In single-particle analysis (SPA), the aim is to obtain a 3D reconstruction of a biological molecule from 2D electron micrographs to the highest level of detail or resolution as possible. Current practice is to collect large volumes of data, hoping to reach high-resolution maps through sheer numbers. However, adding more particles from a specific data set eventually leads to diminishing improvements in resolution. Understanding what these resolution limits are and how to deal with them are important in optimization and automation of SPA. This study revisits the theory of 3D reconstruction and demonstrates how the associated statistics can provide a diagnostic tool to improve SPA. Small numbers of images already give sufficient information on micrograph quality and the amount of data required to reach high resolution. Such feedback allows the microscopist to improve sample-preparation and imaging parameters before committing to extensive data collection. Once a larger data set is available, a B factor can be determined describing the suppression of the signal owing to one or more causes, such as specimen movement, radiation damage, alignment inaccuracy and structural variation. Insight into the causes of signal suppression can then guide the user to consider appropriate actions to obtain better reconstructions.
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Affiliation(s)
- J Bernard Heymann
- Laboratory for Structural Biology Research, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
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44
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Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant. Nat Commun 2018; 9:3628. [PMID: 30194371 PMCID: PMC6128836 DOI: 10.1038/s41467-018-06076-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 08/11/2018] [Indexed: 01/08/2023] Open
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) provides a powerful methodology for structural biologists, but the resolutions typically attained with experimentally determined structures have lagged behind microscope capabilities. Here, we exploit several technical advances to improve resolution, including per-particle contrast transfer function (CTF) refinement and correction for Ewald sphere curvature. The latter is demonstrated with several experimental samples and should become more standard as resolutions increase or at lower microscope accelerating voltages. The combined application of the described methods to micrographs recorded on a Titan Krios enables structure determination at ~1.86-Å resolution of an adeno-associated virus serotype 2 variant (AAV2), an important gene-delivery vehicle. The resulting structural details provide an improved model for understanding the biology of AAV that will guide future vector development for gene therapy. Single-particle cryo-EM is a powerful method for macromolecular structure determination. Here the authors demonstrate that Ewald sphere curvature correction, sub-Angstrom pixilation and per-particle CTF refinement can improve map quality and resolution and present the 1.86 Å cryo-EM structure of an adeno-associated virus serotype 2 variant.
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45
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Cheng A, Eng ET, Alink L, Rice WJ, Jordan KD, Kim LY, Potter CS, Carragher B. High resolution single particle cryo-electron microscopy using beam-image shift. J Struct Biol 2018; 204:270-275. [PMID: 30055234 DOI: 10.1016/j.jsb.2018.07.015] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/21/2018] [Accepted: 07/24/2018] [Indexed: 11/19/2022]
Abstract
Automated data acquisition is used widely for single-particle reconstruction of three-dimensional (3D) volumes of biological complexes preserved in vitreous ice and imaged in a transmission electron microscope. Automation has become integral to this method because of the very large number of particle images required in order to overcome the typically low signal-to-noise ratio of these images. For optimal efficiency, automated data acquisition software packages typically employ some beam-image shift targeting as this method is both fast and accurate (±0.1 µm). In contrast, using only stage movement, relocation to a targeted area under low-dose conditions can only be achieved in combination with multiple iterations or long relaxation times, both reducing efficiency. Nevertheless it is well known that applying beam-image shift induces beam-tilt and with it a potential structure phase error with a phase error π/4 the highest acceptable value. This theory has been used as an argument against beam-image shift for high resolution data collection. Nevertheless, in practice many small beam-image shift datasets have resulted in 3D reconstructions beyond the π/4 phase error limit. To address this apparent contradiction, we performed cryo-EM single-particle reconstructions on a T20S proteasome sample using applied beam-image shifts corresponding to beam tilts from 0 to 10 mrad. To evaluate the results we compared the FSC values, and examined the water density peaks in the 3D map. We conclude that the phase error does not limit the validity of the 3D reconstruction from single-particle averaging beyond the π/4 resolution limit.
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Affiliation(s)
- Anchi Cheng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA.
| | - Edward T Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Lambertus Alink
- Thermo Fisher Scientific, Materials & Structural Analysis, Hillsboro, OR 97124, USA
| | - William J Rice
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA
| | - Kelsey D Jordan
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Laura Y Kim
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA
| | - Clinton S Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA; National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA
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46
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Stagg SM, Mendez JH. Processing apoferritin with the Appion pipeline. J Struct Biol 2018; 204:85-89. [PMID: 29969662 DOI: 10.1016/j.jsb.2018.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/08/2018] [Accepted: 06/29/2018] [Indexed: 01/26/2023]
Abstract
The 3DEM map challenge provided an opportunity to test different algorithms and workflows for processing single particle cryo-EM data. We were interested in testing whether we could use the standard Appion workflow with minimal manual intervention to achieve similar or better resolution than other challengers. Another question we were interested in testing was what the influence of particle sorting and elimination would be on the resolution and quality of 3D reconstructions. Since apoferritin is historically a challenging particle for single particle reconstruction and the authors of the original map challenge data used only a fraction of the particles present in the dataset, we focused on the apoferritin dataset for our entry. We submitted a 3.7 Å map from 25,844 particles and a 3.6 Å map from 53,334 particles and after assessment were among the best of the apoferritin maps that were submitted. Here we present the details of our reconstruction strategy and compare our strategy to that of another high-scoring apoferritin map. Altogether, our results suggest that for a relatively conformationally homogeneous particle like apoferritin, including as many particles as possible after elimination of junk leads to the highest resolution, and the choice of parameters for custom mask creation can lead to subtle but significant changes in the resolution of 3D reconstructions.
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Affiliation(s)
- Scott M Stagg
- Institute of Molecular Biophysics, 91 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States; Department of Chemistry and Biochemistry, 95 Chieftain Way, Florida State University, Tallahassee, FL 32306, United States.
| | - Joshua H Mendez
- Department of Physics, 77 Chieftan Way, Tallahassee, FL 32306, United States
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Quantitative analysis of 3D alignment quality: its impact on soft-validation, particle pruning and homogeneity analysis. Sci Rep 2017; 7:6307. [PMID: 28740215 PMCID: PMC5524947 DOI: 10.1038/s41598-017-06526-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/14/2017] [Indexed: 11/16/2022] Open
Abstract
Single Particle Analysis using cryo-electron microscopy is a structural biology technique aimed at capturing the three-dimensional (3D) conformation of biological macromolecules. Projection images used to construct the 3D density map are characterized by a very low signal-to-noise ratio to minimize radiation damage in the samples. As a consequence, the 3D image alignment process is a challenging and error prone task which usually determines the success or failure of obtaining a high quality map. In this work, we present an approach able to quantify the alignment precision and accuracy of the 3D alignment process, which is then being used to help the reconstruction process in a number of ways, such as: (1) Providing quality indicators of the macromolecular map for soft validation, (2) Assessing the degree of homogeneity of the sample and, (3), Selecting subsets of representative images. We present experimental results in which the quality of the finally obtained 3D maps is clearly improved.
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Sorzano C, Vargas J, Otón J, Abrishami V, de la Rosa-Trevín J, Gómez-Blanco J, Vilas J, Marabini R, Carazo J. A review of resolution measures and related aspects in 3D Electron Microscopy. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 124:1-30. [DOI: 10.1016/j.pbiomolbio.2016.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 08/22/2016] [Accepted: 09/18/2016] [Indexed: 12/21/2022]
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Subramaniam S, Earl LA, Falconieri V, Milne JL, Egelman EH. Resolution advances in cryo-EM enable application to drug discovery. Curr Opin Struct Biol 2016; 41:194-202. [PMID: 27552081 DOI: 10.1016/j.sbi.2016.07.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 12/23/2022]
Abstract
The prospect that the structures of protein assemblies, small and large, can be determined using cryo-electron microscopy (cryo-EM) is beginning to transform the landscape of structural biology and cell biology. Great progress is being made in determining 3D structures of biological assemblies ranging from icosahedral viruses and helical arrays to small membrane proteins and protein complexes. Here, we review recent advances in this field, focusing especially on the emerging use of cryo-EM in mapping the binding of drugs and inhibitors to protein targets, an application that requires structure determination at the highest possible resolutions. We discuss methods used to evaluate the information contained in cryo-EM density maps and consider strengths and weaknesses of approaches currently used to measure map resolution.
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Affiliation(s)
- Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Lesley A Earl
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Veronica Falconieri
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jacqueline Ls Milne
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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