101
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Ravelli RBG, Nijpels FJT, Henderikx RJM, Weissenberger G, Thewessem S, Gijsbers A, Beulen BWAMM, López-Iglesias C, Peters PJ. Cryo-EM structures from sub-nl volumes using pin-printing and jet vitrification. Nat Commun 2020; 11:2563. [PMID: 32444637 PMCID: PMC7244535 DOI: 10.1038/s41467-020-16392-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 04/17/2020] [Indexed: 01/17/2023] Open
Abstract
The increasing demand for cryo-electron microscopy (cryo-EM) reveals drawbacks in current sample preparation protocols, such as sample waste and lack of reproducibility. Here, we present several technical developments that provide efficient sample preparation for cryo-EM studies. Pin printing substantially reduces sample waste by depositing only a sub-nanoliter volume of sample on the carrier surface. Sample evaporation is mitigated by dewpoint control feedback loops. The deposited sample is vitrified by jets of cryogen followed by submersion into a cryogen bath. Because the cryogen jets cool the sample from the center, premounted autogrids can be used and loaded directly into automated cryo-EMs. We integrated these steps into a single device, named VitroJet. The device’s performance was validated by resolving four standard proteins (apoferritin, GroEL, worm hemoglobin, beta-galactosidase) to ~3 Å resolution using a 200-kV electron microscope. The VitroJet offers a promising solution for improved automated sample preparation in cryo-EM studies. There is a need to further improve the automation of cryo-EM sample preparation to make it more easily accessible for non-specialists, reduce sample waste and increase reproducibility. Here, the authors present VitroJet, a single device, where sub-nl volumes of samples are deposited by pin printing thus eliminating the need for sample blotting, which is followed by jet vitrification, and they show that high-resolution structures can be obtained using four standard proteins.
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Affiliation(s)
- Raimond B G Ravelli
- The Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, Netherlands.
| | - Frank J T Nijpels
- The Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, Netherlands.,CryoSol-World, Maastricht, Netherlands
| | - Rene J M Henderikx
- The Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, Netherlands.,CryoSol-World, Maastricht, Netherlands
| | - Giulia Weissenberger
- The Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, Netherlands.,CryoSol-World, Maastricht, Netherlands
| | - Sanne Thewessem
- Instrument Development, Engineering and Evaluation (IDEE), Maastricht University, Maastricht, Netherlands
| | - Abril Gijsbers
- The Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, Netherlands
| | - Bart W A M M Beulen
- CryoSol-World, Maastricht, Netherlands.,Instrument Development, Engineering and Evaluation (IDEE), Maastricht University, Maastricht, Netherlands
| | - Carmen López-Iglesias
- The Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, Netherlands
| | - Peter J Peters
- The Maastricht Multimodal Molecular Imaging Institute (M4i), Division of Nanoscopy, Maastricht University, Maastricht, Netherlands. .,CryoSol-World, Maastricht, Netherlands.
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102
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Hamdi F, Tüting C, Semchonok DA, Visscher KM, Kyrilis FL, Meister A, Skalidis I, Schmidt L, Parthier C, Stubbs MT, Kastritis PL. 2.7 Å cryo-EM structure of vitrified M. musculus H-chain apoferritin from a compact 200 keV cryo-microscope. PLoS One 2020; 15:e0232540. [PMID: 32374767 PMCID: PMC7202636 DOI: 10.1371/journal.pone.0232540] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 04/16/2020] [Indexed: 12/28/2022] Open
Abstract
Here we present the structure of mouse H-chain apoferritin at 2.7 Å (FSC = 0.143) solved by single particle cryogenic electron microscopy (cryo-EM) using a 200 kV device, the Thermo Fisher Glacios®. This is a compact, two-lens illumination system with a constant power objective lens, without any energy filters or aberration correctors, often thought of as a "screening cryo-microscope". Coulomb potential maps reveal clear densities for main chain carbonyl oxygens, residue side chains (including alternative conformations) and bound solvent molecules. We used a quasi-crystallographic reciprocal space approach to fit model coordinates to the experimental cryo-EM map. We argue that the advantages offered by (a) the high electronic and mechanical stability of the microscope, (b) the high emission stability and low beam energy spread of the high brightness Field Emission Gun (X-FEG), (c) direct electron detection technology and (d) particle-based Contrast Transfer Function (CTF) refinement have contributed to achieving high resolution. Overall, we show that basic electron optical settings for automated cryo-electron microscopy imaging can be used to determine structures approaching atomic resolution.
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Affiliation(s)
- Farzad Hamdi
- ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Christian Tüting
- ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Dmitry A. Semchonok
- ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Koen M. Visscher
- AIMMS Division of Molecular Toxicology, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Fotis L. Kyrilis
- ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Annette Meister
- ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Ioannis Skalidis
- ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Lisa Schmidt
- ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Christoph Parthier
- Institute of Biochemistry and Biotechnology, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Milton T. Stubbs
- ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Panagiotis L. Kastritis
- ZIK HALOmem, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Charles-Tanford-Proteinzentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
- ZIK HALOmem, Biozentrum, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
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103
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Structure of severe fever with thrombocytopenia syndrome virus L protein elucidates the mechanisms of viral transcription initiation. Nat Microbiol 2020; 5:864-871. [PMID: 32341479 DOI: 10.1038/s41564-020-0712-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/19/2020] [Indexed: 02/07/2023]
Abstract
Segmented negative-sense RNA viruses (sNSRVs) encode a single-polypeptide polymerase (L protein) or a heterotrimeric polymerase complex to cannibalize host messenger RNA cap structures serving as primers of transcription, and catalyse RNA synthesis. Here, we report the full-length structure of the severe fever with thrombocytopaenia syndrome virus (SFTSV) L protein, as determined by cryogenic electron microscopy at 3.4 Å, leading to an atomic model harbouring three functional parts (an endonuclease, an RNA-dependent RNA polymerase and a cap-binding domain) and two structural domains (an arm domain with a blocker motif and a carboxy-terminal lariat domain). The SFTSV L protein has a compact architecture in which its cap-binding pocket is surprisingly occupied by an Arg finger of the blocker motif, and the endonuclease active centre faces back towards the cap-binding pocket, suggesting that domain rearrangements are necessary to acquire the pre-initiation state of the active site. Our results provide insight into the complete architecture of sNSRV-encoded L protein and further the understanding of sNSRV transcription initiation.
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104
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Michael AK, Grand RS, Isbel L, Cavadini S, Kozicka Z, Kempf G, Bunker RD, Schenk AD, Graff-Meyer A, Pathare GR, Weiss J, Matsumoto S, Burger L, Schübeler D, Thomä NH. Mechanisms of OCT4-SOX2 motif readout on nucleosomes. Science 2020; 368:1460-1465. [PMID: 32327602 DOI: 10.1126/science.abb0074] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022]
Abstract
Transcription factors (TFs) regulate gene expression through chromatin where nucleosomes restrict DNA access. To study how TFs bind nucleosome-occupied motifs, we focused on the reprogramming factors OCT4 and SOX2 in mouse embryonic stem cells. We determined TF engagement throughout a nucleosome at base-pair resolution in vitro, enabling structure determination by cryo-electron microscopy at two preferred positions. Depending on motif location, OCT4 and SOX2 differentially distort nucleosomal DNA. At one position, OCT4-SOX2 removes DNA from histone H2A and histone H3; however, at an inverted motif, the TFs only induce local DNA distortions. OCT4 uses one of its two DNA-binding domains to engage DNA in both structures, reading out a partial motif. These findings explain site-specific nucleosome engagement by the pluripotency factors OCT4 and SOX2, and they reveal how TFs distort nucleosomes to access chromatinized motifs.
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Affiliation(s)
- Alicia K Michael
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Zuzanna Kozicka
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,Faculty of Science, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Richard D Bunker
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Andreas D Schenk
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Alexandra Graff-Meyer
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Ganesh R Pathare
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Joscha Weiss
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Syota Matsumoto
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland. .,Faculty of Science, University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.
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105
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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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106
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Alcón P, Shakeel S, Chen ZA, Rappsilber J, Patel KJ, Passmore LA. FANCD2-FANCI is a clamp stabilized on DNA by monoubiquitination of FANCD2 during DNA repair. Nat Struct Mol Biol 2020; 27:240-248. [PMID: 32066963 PMCID: PMC7067600 DOI: 10.1038/s41594-020-0380-1] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/14/2020] [Indexed: 01/18/2023]
Abstract
Vertebrate DNA crosslink repair excises toxic replication-blocking DNA crosslinks. Numerous factors involved in crosslink repair have been identified, and mutations in their corresponding genes cause Fanconi anemia (FA). A key step in crosslink repair is monoubiquitination of the FANCD2-FANCI heterodimer, which then recruits nucleases to remove the DNA lesion. Here, we use cryo-EM to determine the structures of recombinant chicken FANCD2 and FANCI complexes. FANCD2-FANCI adopts a closed conformation when the FANCD2 subunit is monoubiquitinated, creating a channel that encloses double-stranded DNA (dsDNA). Ubiquitin is positioned at the interface of FANCD2 and FANCI, where it acts as a covalent molecular pin to trap the complex on DNA. In contrast, isolated FANCD2 is a homodimer that is unable to bind DNA, suggestive of an autoinhibitory mechanism that prevents premature activation. Together, our work suggests that FANCD2-FANCI is a clamp that is locked onto DNA by ubiquitin, with distinct interfaces that may recruit other DNA repair factors.
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Affiliation(s)
- Pablo Alcón
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Zhuo A Chen
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
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107
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Wu M, Lander GC, Herzik MA. Sub-2 Angstrom resolution structure determination using single-particle cryo-EM at 200 keV. J Struct Biol X 2020; 4:100020. [PMID: 32647824 PMCID: PMC7337053 DOI: 10.1016/j.yjsbx.2020.100020] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 11/30/2022] Open
Abstract
Although the advent of direct electron detectors (DEDs) and software developments have enabled the routine use of single-particle cryogenic electron microscopy (cryo-EM) for structure determination of well-behaved specimens to high-resolution, there nonetheless remains a discrepancy between the resolutions attained for biological specimens and the information limits of modern transmission electron microscopes (TEMs). Instruments operating at 300 kV equipped with DEDs are the current paradigm for high-resolution single-particle cryo-EM, while 200 kV TEMs remain comparatively underutilized for purposes beyond sample screening. Here, we expand upon our prior work and demonstrate that one such 200 kV microscope, the Talos Arctica, equipped with a K2 DED is capable of determining structures of macromolecules to as high as ∼1.7 Å resolution. At this resolution, ordered water molecules are readily assigned and holes in aromatic residues can be clearly distinguished in the reconstructions. This work emphasizes the utility of 200 kV electrons for high-resolution single-particle cryo-EM and applications such as structure-based drug design.
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Affiliation(s)
- Mengyu Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Gabriel C. Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Mark A. Herzik
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, United States
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108
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Uchański T, Pardon E, Steyaert J. Nanobodies to study protein conformational states. Curr Opin Struct Biol 2020; 60:117-123. [DOI: 10.1016/j.sbi.2020.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 01/07/2023]
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109
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Vilas JL, Tagare HD, Vargas J, Carazo JM, Sorzano COS. Measuring local-directional resolution and local anisotropy in cryo-EM maps. Nat Commun 2020; 11:55. [PMID: 31896756 PMCID: PMC6940361 DOI: 10.1038/s41467-019-13742-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/18/2019] [Indexed: 12/17/2022] Open
Abstract
The introduction of local resolution has enormously helped the understanding of cryo-EM maps. Still, for any given pixel it is a global, aggregated value, that makes impossible the individual analysis of the contribution of the different projection directions. We introduce MonoDir, a fully automatic, parameter-free method that, starting only from the final cryo-EM map, decomposes local resolution into the different projection directions, providing a detailed level of analysis of the final map. Many applications of directional local resolution are possible, and we concentrate here on map quality and validation. It is important to analyse the local resolution of cryo-EM maps. Here the authors present MonoDir, a fully automatic and parameter free method for the directional local resolution analysis of cryo-EM maps that requires only the final map as input and they also propose indicators for assessing map quality.
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Affiliation(s)
- Jose Luis Vilas
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Campus Universidad Autonoma, 28049, Cantoblanco, Madrid, Spain
| | - Hemant D Tagare
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
| | - Javier Vargas
- Department of Anatomy and Cell Biology, McGill University, Montreal, H3A 0G4, Canada
| | - Jose Maria Carazo
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Campus Universidad Autonoma, 28049, Cantoblanco, Madrid, Spain.
| | - Carlos Oscar S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnologia (CNB-CSIC), Campus Universidad Autonoma, 28049, Cantoblanco, Madrid, Spain.
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110
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Kalienkova V, Alvadia C, Clerico Mosina V, Paulino C. Single-Particle Cryo-EM of Membrane Proteins in Lipid Nanodiscs. Methods Mol Biol 2020; 2127:245-273. [PMID: 32112327 DOI: 10.1007/978-1-0716-0373-4_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Single-particle cryo-electron microscopy has become an indispensable technique in structural biology. In particular when studying membrane proteins, it allows the use of membrane-mimicking tools, which can be crucial for a comprehensive understanding of the structure-function relationship of the protein in its native environment. In this chapter we focus on the application of nanodiscs and use our recent studies on the TMEM16 family as an example.
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Affiliation(s)
- Valeria Kalienkova
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Carolina Alvadia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Vanessa Clerico Mosina
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Cristina Paulino
- Department of Structural Biology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
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111
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Brillault L, Landsberg MJ. Preparation of Proteins and Macromolecular Assemblies for Cryo-electron Microscopy. Methods Mol Biol 2020; 2073:221-246. [PMID: 31612445 DOI: 10.1007/978-1-4939-9869-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cryo-electron microscopy has become popular as the penultimate step on the road to structure determination for many proteins and macromolecular assemblies. The process of obtaining high-resolution images of a purified biomolecular complex in an electron microscope often follows a long, and in many cases exhaustive screening process in which many iterative rounds of protein purification are employed and the sample preparation procedure progressively re-evaluated in order to improve the distribution of particles visualized under the electron microscope, and thus maximize the opportunity for high-resolution structure determination. Typically, negative stain electron microscopy is employed to obtain a preliminary assessment of the sample quality, followed by cryo-EM which first requires the identification of optimal vitrification conditions. The original methods for frozen-hydrated specimen preparation developed over 40 years ago still enjoy widespread use today, although recent developments have set the scene for a future where more systematic and high-throughput approaches to the preparation of vitrified biomolecular complexes may be routinely employed. Here we summarize current approaches and ongoing innovations for the preparation of frozen-hydrated single particle specimens for cryo-EM, highlighting some of the commonly encountered problems and approaches that may help overcome these.
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Affiliation(s)
- Lou Brillault
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
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112
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Shakeel S, Rajendra E, Alcón P, O'Reilly F, Chorev DS, Maslen S, Degliesposti G, Russo CJ, He S, Hill CH, Skehel JM, Scheres SHW, Patel KJ, Rappsilber J, Robinson CV, Passmore LA. Structure of the Fanconi anaemia monoubiquitin ligase complex. Nature 2019; 575:234-237. [PMID: 31666700 PMCID: PMC6858856 DOI: 10.1038/s41586-019-1703-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/18/2019] [Indexed: 11/17/2022]
Abstract
The Fanconi anaemia (FA) pathway repairs DNA damage caused by endogenous and chemotherapy-induced DNA crosslinks, and responds to replication stress1,2. Genetic inactivation of this pathway by mutation of genes encoding FA complementation group (FANC) proteins impairs development, prevents blood production and promotes cancer1,3. The key molecular step in the FA pathway is the monoubiquitination of a pseudosymmetric heterodimer of FANCD2-FANCI4,5 by the FA core complex-a megadalton multiprotein E3 ubiquitin ligase6,7. Monoubiquitinated FANCD2 then recruits additional protein factors to remove the DNA crosslink or to stabilize the stalled replication fork. A molecular structure of the FA core complex would explain how it acts to maintain genome stability. Here we reconstituted an active, recombinant FA core complex, and used cryo-electron microscopy and mass spectrometry to determine its structure. The FA core complex comprises two central dimers of the FANCB and FA-associated protein of 100 kDa (FAAP100) subunits, flanked by two copies of the RING finger subunit, FANCL. These two heterotrimers act as a scaffold to assemble the remaining five subunits, resulting in an extended asymmetric structure. Destabilization of the scaffold would disrupt the entire complex, resulting in a non-functional FA pathway. Thus, the structure provides a mechanistic basis for the low numbers of patients with mutations in FANCB, FANCL and FAAP100. Despite a lack of sequence homology, FANCB and FAAP100 adopt similar structures. The two FANCL subunits are in different conformations at opposite ends of the complex, suggesting that each FANCL has a distinct role. This structural and functional asymmetry of dimeric RING finger domains may be a general feature of E3 ligases. The cryo-electron microscopy structure of the FA core complex provides a foundation for a detailed understanding of its E3 ubiquitin ligase activity and DNA interstrand crosslink repair.
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Affiliation(s)
| | | | - Pablo Alcón
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Francis O'Reilly
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Shaoda He
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Chris H Hill
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | | | - Juri Rappsilber
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
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113
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Naydenova K, McMullan G, Peet MJ, Lee Y, Edwards PC, Chen S, Leahy E, Scotcher S, Henderson R, Russo CJ. CryoEM at 100 keV: a demonstration and prospects. IUCRJ 2019; 6:1086-1098. [PMID: 31709064 PMCID: PMC6830209 DOI: 10.1107/s2052252519012612] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/10/2019] [Indexed: 05/23/2023]
Abstract
100 kV is investigated as the operating voltage for single-particle electron cryomicroscopy (cryoEM). Reducing the electron energy from the current standard of 300 or 200 keV offers both cost savings and potentially improved imaging. The latter follows from recent measurements of radiation damage to biological specimens by high-energy electrons, which show that at lower energies there is an increased amount of information available per unit damage. For frozen hydrated specimens around 300 Å in thickness, the predicted optimal electron energy for imaging is 100 keV. Currently available electron cryomicroscopes in the 100-120 keV range are not optimized for cryoEM as they lack both the spatially coherent illumination needed for the high defocus used in cryoEM and imaging detectors optimized for 100 keV electrons. To demonstrate the potential of imaging at 100 kV, the voltage of a standard, commercial 200 kV field-emission gun (FEG) microscope was reduced to 100 kV and a side-entry cryoholder was used. As high-efficiency, large-area cameras are not currently available for 100 keV electrons, a commercial hybrid pixel camera designed for X-ray detection was attached to the camera chamber and was used for low-dose data collection. Using this configuration, five single-particle specimens were imaged: hepatitis B virus capsid, bacterial 70S ribosome, catalase, DNA protection during starvation protein and haemoglobin, ranging in size from 4.5 MDa to 64 kDa with corresponding diameters from 320 to 72 Å. These five data sets were used to reconstruct 3D structures with resolutions between 8.4 and 3.4 Å. Based on this work, the practical advantages and current technological limitations to single-particle cryoEM at 100 keV are considered. These results are also discussed in the context of future microscope development towards the goal of rapid, simple and widely available structure determination of any purified biological specimen.
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Affiliation(s)
- K. Naydenova
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - G. McMullan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - M. J. Peet
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - Y. Lee
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - P. C. Edwards
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - S. Chen
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - E. Leahy
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - S. Scotcher
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - R. Henderson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - C. J. Russo
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
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114
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Anandapadamanaban M, Masson GR, Perisic O, Berndt A, Kaufman J, Johnson CM, Santhanam B, Rogala KB, Sabatini DM, Williams RL. Architecture of human Rag GTPase heterodimers and their complex with mTORC1. Science 2019; 366:203-210. [PMID: 31601764 PMCID: PMC6795536 DOI: 10.1126/science.aax3939] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 09/03/2019] [Indexed: 12/11/2022]
Abstract
The Rag guanosine triphosphatases (GTPases) recruit the master kinase mTORC1 to lysosomes to regulate cell growth and proliferation in response to amino acid availability. The nucleotide state of Rag heterodimers is critical for their association with mTORC1. Our cryo-electron microscopy structure of RagA/RagC in complex with mTORC1 shows the details of RagA/RagC binding to the RAPTOR subunit of mTORC1 and explains why only the RagAGTP/RagCGDP nucleotide state binds mTORC1. Previous kinetic studies suggested that GTP binding to one Rag locks the heterodimer to prevent GTP binding to the other. Our crystal structures and dynamics of RagA/RagC show the mechanism for this locking and explain how oncogenic hotspot mutations disrupt this process. In contrast to allosteric activation by RHEB, Rag heterodimer binding does not change mTORC1 conformation and activates mTORC1 by targeting it to lysosomes.
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Affiliation(s)
| | - Glenn R Masson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Olga Perisic
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Alex Berndt
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | | | - Kacper B Rogala
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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115
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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: 34] [Impact Index Per Article: 6.8] [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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116
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Wilkinson ME, Kumar A, Casañal A. Methods for merging data sets in electron cryo-microscopy. Acta Crystallogr D Struct Biol 2019; 75:782-791. [PMID: 31478901 PMCID: PMC6719665 DOI: 10.1107/s2059798319010519] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 07/23/2019] [Indexed: 11/26/2022] Open
Abstract
Recent developments have resulted in electron cryo-microscopy (cryo-EM) becoming a useful tool for the structure determination of biological macromolecules. For samples containing inherent flexibility, heterogeneity or preferred orientation, the collection of extensive cryo-EM data using several conditions and microscopes is often required. In such a scenario, merging cryo-EM data sets is advantageous because it allows improved three-dimensional reconstructions to be obtained. Since data sets are not always collected with the same pixel size, merging data can be challenging. Here, two methods to combine cryo-EM data are described. Both involve the calculation of a rescaling factor from independent data sets. The effects of errors in the scaling factor on the results of data merging are also estimated. The methods described here provide a guideline for cryo-EM users who wish to combine data sets from the same type of microscope and detector.
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Affiliation(s)
- Max E. Wilkinson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Ananthanarayanan Kumar
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
| | - Ana Casañal
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England
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117
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Fan H, Walker AP, Carrique L, Keown JR, Serna Martin I, Karia D, Sharps J, Hengrung N, Pardon E, Steyaert J, Grimes JM, Fodor E. Structures of influenza A virus RNA polymerase offer insight into viral genome replication. Nature 2019; 573:287-290. [PMID: 31485076 PMCID: PMC6795553 DOI: 10.1038/s41586-019-1530-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/07/2019] [Indexed: 12/24/2022]
Abstract
Influenza A viruses are responsible for seasonal epidemics, and pandemics can arise from the transmission of novel zoonotic influenza A viruses to humans1,2. Influenza A viruses contain a segmented negative-sense RNA genome, which is transcribed and replicated by the viral-RNA-dependent RNA polymerase (FluPolA) composed of PB1, PB2 and PA subunits3-5. Although the high-resolution crystal structure of FluPolA of bat influenza A virus has previously been reported6, there are no complete structures available for human and avian FluPolA. Furthermore, the molecular mechanisms of genomic viral RNA (vRNA) replication-which proceeds through a complementary RNA (cRNA) replicative intermediate, and requires oligomerization of the polymerase7-10-remain largely unknown. Here, using crystallography and cryo-electron microscopy, we determine the structures of FluPolA from human influenza A/NT/60/1968 (H3N2) and avian influenza A/duck/Fujian/01/2002 (H5N1) viruses at a resolution of 3.0-4.3 Å, in the presence or absence of a cRNA or vRNA template. In solution, FluPolA forms dimers of heterotrimers through the C-terminal domain of the PA subunit, the thumb subdomain of PB1 and the N1 subdomain of PB2. The cryo-electron microscopy structure of monomeric FluPolA bound to the cRNA template reveals a binding site for the 3' cRNA at the dimer interface. We use a combination of cell-based and in vitro assays to show that the interface of the FluPolA dimer is required for vRNA synthesis during replication of the viral genome. We also show that a nanobody (a single-domain antibody) that interferes with FluPolA dimerization inhibits the synthesis of vRNA and, consequently, inhibits virus replication in infected cells. Our study provides high-resolution structures of medically relevant FluPolA, as well as insights into the replication mechanisms of the viral RNA genome. In addition, our work identifies sites in FluPolA that could be targeted in the development of antiviral drugs.
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Affiliation(s)
- Haitian Fan
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | | | - Loïc Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jeremy R Keown
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Itziar Serna Martin
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Dimple Karia
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jane Sharps
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Narin Hengrung
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Francis Crick Institute, London, UK
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Diamond Light Source, Didcot, UK.
| | - Ervin Fodor
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
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118
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Meng R, Jiang M, Cui Z, Chang JY, Yang K, Jakana J, Yu X, Wang Z, Hu B, Zhang J. Structural basis for the adsorption of a single-stranded RNA bacteriophage. Nat Commun 2019; 10:3130. [PMID: 31311931 PMCID: PMC6635492 DOI: 10.1038/s41467-019-11126-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/24/2019] [Indexed: 12/31/2022] Open
Abstract
Single-stranded RNA bacteriophages (ssRNA phages) infect Gram-negative bacteria via a single maturation protein (Mat), which attaches to a retractile pilus of the host. Here we present structures of the ssRNA phage MS2 in complex with the Escherichia coli F-pilus, showing a network of hydrophobic and electrostatic interactions at the Mat-pilus interface. Moreover, binding of the pilus induces slight orientational variations of the Mat relative to the rest of the phage capsid, priming the Mat-connected genomic RNA (gRNA) for its release from the virions. The exposed tip of the attached Mat points opposite to the direction of the pilus retraction, which may facilitate the translocation of the gRNA from the capsid into the host cytosol. In addition, our structures determine the orientation of the assembled F-pilin subunits relative to the cell envelope, providing insights into the F-like type IV secretion systems.
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Affiliation(s)
- Ran Meng
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Mengqiu Jiang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Zhicheng Cui
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Jeng-Yih Chang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Kailu Yang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
- Howard Hughes Medical Institute, Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Joanita Jakana
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xinzhe Yu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhao Wang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bo Hu
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA.
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119
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Yao Q, Weaver SJ, Mock JY, Jensen GJ. Fusion of DARPin to Aldolase Enables Visualization of Small Protein by Cryo-EM. Structure 2019; 27:1148-1155.e3. [PMID: 31080120 PMCID: PMC6610650 DOI: 10.1016/j.str.2019.04.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 03/04/2019] [Accepted: 04/05/2019] [Indexed: 12/21/2022]
Abstract
Solving protein structures by single-particle cryoelectron microscopy (cryo-EM) has become a crucial tool in structural biology. While exciting progress is being made toward the visualization of small macromolecules, the median protein size in both eukaryotes and bacteria is still beyond the reach of cryo-EM. To overcome this problem, we implemented a platform strategy in which a small protein target was rigidly attached to a large, symmetric base via a selectable adapter. Of our seven designs, the best construct used a designed ankyrin repeat protein (DARPin) rigidly fused to tetrameric rabbit muscle aldolase through a helical linker. The DARPin retained its ability to bind its target: GFP. We solved the structure of this complex to 3.0 Å resolution overall, with 5-8 Å resolution in the GFP region. As flexibility in the DARPin position limited the overall resolution of the target, we describe strategies to rigidify this element.
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Affiliation(s)
- Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Sara J Weaver
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Jee-Young Mock
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA; Howard Hughes Medical Institute, 1200 E. California Boulevard, Pasadena, CA 91125, USA.
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120
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Gordiyenko Y, Llácer JL, Ramakrishnan V. Structural basis for the inhibition of translation through eIF2α phosphorylation. Nat Commun 2019; 10:2640. [PMID: 31201334 PMCID: PMC6572841 DOI: 10.1038/s41467-019-10606-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/10/2019] [Indexed: 11/29/2022] Open
Abstract
One of the responses to stress by eukaryotic cells is the down-regulation of protein synthesis by phosphorylation of translation initiation factor eIF2. Phosphorylation results in low availability of the eIF2 ternary complex (eIF2-GTP-tRNAi) by affecting the interaction of eIF2 with its GTP-GDP exchange factor eIF2B. We have determined the cryo-EM structure of yeast eIF2B in complex with phosphorylated eIF2 at an overall resolution of 4.2 Å. Two eIF2 molecules bind opposite sides of an eIF2B hetero-decamer through eIF2α-D1, which contains the phosphorylated Ser51. eIF2α-D1 is mainly inserted between the N-terminal helix bundle domains of δ and α subunits of eIF2B. Phosphorylation of Ser51 enhances binding to eIF2B through direct interactions of phosphate groups with residues in eIF2Bα and indirectly by inducing contacts of eIF2α helix 58–63 with eIF2Bδ leading to a competition with Met-tRNAi. During stress, protein synthesis is inhibited through phosphorylation of the initiation factor eIF2 on its alpha subunit and its interaction with eIF2B. Here the authors describe a structure of the yeast eIF2B in complex with its substrate - the GDP-bound phosphorylated eIF2, providing insights into how phosphorylation results in a tighter interaction with eIF2B.
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Affiliation(s)
- Yuliya Gordiyenko
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - José Luis Llácer
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK. .,Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas and CIBERER-ISCIII, Valencia, 46010, Spain.
| | - V Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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121
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Fan X, Wang J, Zhang X, Yang Z, Zhang JC, Zhao L, Peng HL, Lei J, Wang HW. Single particle cryo-EM reconstruction of 52 kDa streptavidin at 3.2 Angstrom resolution. Nat Commun 2019; 10:2386. [PMID: 31160591 PMCID: PMC6546690 DOI: 10.1038/s41467-019-10368-w] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/06/2019] [Indexed: 11/09/2022] Open
Abstract
The fast development of single-particle cryogenic electron microscopy (cryo-EM) has made it more feasible to obtain the 3D structure of well-behaved macromolecules with a molecular weight higher than 300 kDa at ~3 Å resolution. However, it remains a challenge to obtain the high-resolution structures of molecules smaller than 200 kDa using single-particle cryo-EM. In this work, we apply the Cs-corrector-VPP-coupled cryo-EM to study the 52 kDa streptavidin (SA) protein supported on a thin layer of graphene and embedded in vitreous ice. We are able to solve both the apo-SA and biotin-bound SA structures at near-atomic resolution using single-particle cryo-EM. We demonstrate that the method has the potential to determine the structures of molecules as small as 39 kDa. It remains a challenge to obtain high-resolution structures of molecules smaller than 200 kDa using single particle cryo-EM. Here, the authors apply the Cs-corrector-VPP coupled cryo-EM and solve structures of the 52 kDa streptavidin (SA) protein at near-atomic resolution.
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Affiliation(s)
- Xiao Fan
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jia Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xing Zhang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zi Yang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jin-Can Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Lingyun Zhao
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Hai-Lin Peng
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Jianlin Lei
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center of Biological Structures, School of Life Sciences, Tsinghua University, Beijing, 100084, China. .,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
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122
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Kouba T, Drncová P, Cusack S. Structural snapshots of actively transcribing influenza polymerase. Nat Struct Mol Biol 2019; 26:460-470. [PMID: 31160782 PMCID: PMC7610713 DOI: 10.1038/s41594-019-0232-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/18/2019] [Indexed: 12/15/2022]
Abstract
Influenza virus RNA-dependent RNA polymerase uses unique mechanisms to transcribe its single-stranded genomic viral RNA (vRNA) into messenger RNA. The polymerase is initially bound to a promoter comprising the partially base-paired 3' and 5' extremities of the RNA. A short, capped primer, 'cap-snatched' from a nascent host polymerase II transcript, is directed towards the polymerase active site to initiate RNA synthesis. Here we present structural snapshots, as determined by X-ray crystallography and cryo-electron microscopy, of actively initiating influenza polymerase as it transitions towards processive elongation. Unexpected conformational changes unblock the active site cavity to allow establishment of a nine-base-pair template-product RNA duplex before the strands separate into distinct exit channels. Concomitantly, as the template translocates, the promoter base pairs are broken and the template entry region is remodeled. These structures reveal details of the influenza polymerase active site that will help optimize nucleoside analogs or other compounds that directly inhibit viral RNA synthesis.
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Affiliation(s)
- Tomas Kouba
- European Molecular Biology Laboratory, Grenoble, France
| | - Petra Drncová
- European Molecular Biology Laboratory, Grenoble, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble, France.
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123
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Abstract
Single-particle electron cryomicroscopy (cryoEM) has now proved to be the method of choice for determining the structure of biological macromolecules and complexes. Yet success in determining a structure by cryoEM depends on being able to prepare a frozen specimen on a small metal support called a grid. This process is poorly controlled at present because of molecule–surface interactions. Here we used a modified form of graphene, in conjunction with a stable grid made of gold, to control these surface effects. Functionalized graphene-on-gold grids improve the reliability of specimen preparation and enhance image quality. This technology has the potential to take specimen preparation for cryoEM from a trial and error art to a controlled and reproducible process. With recent technological advances, the atomic resolution structure of any purified biomolecular complex can, in principle, be determined by single-particle electron cryomicroscopy (cryoEM). In practice, the primary barrier to structure determination is the preparation of a frozen specimen suitable for high-resolution imaging. To address this, we present a multifunctional specimen support for cryoEM, comprising large-crystal monolayer graphene suspended across the surface of an ultrastable gold specimen support. Using a low-energy plasma surface modification system, we tune the surface of this support to the specimen by patterning a range of covalent functionalizations across the graphene layer on a single grid. This support design reduces specimen movement during imaging, improves image quality, and allows high-resolution structure determination with a minimum of material and data.
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124
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Danev R, Yanagisawa H, Kikkawa M. Cryo-Electron Microscopy Methodology: Current Aspects and Future Directions. Trends Biochem Sci 2019; 44:837-848. [PMID: 31078399 DOI: 10.1016/j.tibs.2019.04.008] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/08/2019] [Accepted: 04/12/2019] [Indexed: 01/01/2023]
Abstract
Cryo-electron microscopy (cryo-EM) has emerged as a powerful structure determination technique. Its most prolific branch is single particle analysis (SPA), a method being used in a growing number of laboratories worldwide to determine high-resolution protein structures. Cryo-electron tomography (cryo-ET) is another powerful approach that enables visualization of protein complexes in their native cellular environment. Despite the wide-ranging success of cryo-EM, there are many methodological aspects that could be improved. Those include sample preparation, sample screening, data acquisition, image processing, and structure validation. Future developments will increase the reliability and throughput of the technique and reduce the cost and skill level barrier for its adoption.
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Affiliation(s)
- Radostin Danev
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Haruaki Yanagisawa
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masahide Kikkawa
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
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125
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Morris KL, Buffalo CZ, Stürzel CM, Heusinger E, Kirchhoff F, Ren X, Hurley JH. HIV-1 Nefs Are Cargo-Sensitive AP-1 Trimerization Switches in Tetherin Downregulation. Cell 2019; 174:659-671.e14. [PMID: 30053425 DOI: 10.1016/j.cell.2018.07.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/27/2018] [Accepted: 07/03/2018] [Indexed: 01/08/2023]
Abstract
The HIV accessory protein Nef counteracts immune defenses by subverting coated vesicle pathways. The 3.7 Å cryo-EM structure of a closed trimer of the clathrin adaptor AP-1, the small GTPase Arf1, HIV-1 Nef, and the cytosolic tail of the restriction factor tetherin suggested a mechanism for inactivating tetherin by Golgi retention. The 4.3 Å structure of a mutant Nef-induced dimer of AP-1 showed how the closed trimer is regulated by the dileucine loop of Nef. HDX-MS and mutational analysis were used to show how cargo dynamics leads to alternative Arf1 trimerization, directing Nef targets to be either retained at the trans-Golgi or sorted to lysosomes. Phosphorylation of the NL4-3 M-Nef was shown to regulate AP-1 trimerization, explaining how O-Nefs lacking this phosphosite counteract tetherin but most M-Nefs do not. These observations show how the higher-order organization of a vesicular coat can be allosterically modulated to direct cargoes to distinct fates.
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Affiliation(s)
- Kyle L Morris
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cosmo Z Buffalo
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Elena Heusinger
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Xuefeng Ren
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - James H Hurley
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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126
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D'Imprima E, Floris D, Joppe M, Sánchez R, Grininger M, Kühlbrandt W. Protein denaturation at the air-water interface and how to prevent it. eLife 2019; 8:42747. [PMID: 30932812 PMCID: PMC6443348 DOI: 10.7554/elife.42747] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/27/2019] [Indexed: 12/19/2022] Open
Abstract
Electron cryo-microscopy analyzes the structure of proteins and protein complexes in vitrified solution. Proteins tend to adsorb to the air-water interface in unsupported films of aqueous solution, which can result in partial or complete denaturation. We investigated the structure of yeast fatty acid synthase at the air-water interface by electron cryo-tomography and single-particle image processing. Around 90% of complexes adsorbed to the air-water interface are partly denatured. We show that the unfolded regions face the air-water interface. Denaturation by contact with air may happen at any stage of specimen preparation. Denaturation at the air-water interface is completely avoided when the complex is plunge-frozen on a substrate of hydrophilized graphene.
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Affiliation(s)
- Edoardo D'Imprima
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Davide Floris
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Mirko Joppe
- Buchmann Institute for Molecular Life Sciences, Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt, Germany
| | - Ricardo Sánchez
- Sofja Kovalevskaja Group, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Martin Grininger
- Buchmann Institute for Molecular Life Sciences, Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
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127
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Abstract
Cryogenic electron microscopy (cryo-EM) enables structure determination of macromolecular objects and their assemblies. Although the techniques have been developing for nearly four decades, they have gained widespread attention in recent years due to technical advances on numerous fronts, enabling traditional microscopists to break into the world of molecular structural biology. Many samples can now be routinely analyzed at near-atomic resolution using standard imaging and image analysis techniques. However, numerous challenges to conventional workflows remain, and continued technical advances open entirely novel opportunities for discovery and exploration. Here, I will review some of the main methods surrounding cryo-EM with an emphasis specifically on single-particle analysis, and I will highlight challenges, open questions, and opportunities for methodology development.
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Affiliation(s)
- Dmitry Lyumkis
- From the Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, California 92037
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128
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Hill CH, Boreikaitė V, Kumar A, Casañal A, Kubík P, Degliesposti G, Maslen S, Mariani A, von Loeffelholz O, Girbig M, Skehel M, Passmore LA. Activation of the Endonuclease that Defines mRNA 3' Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex. Mol Cell 2019; 73:1217-1231.e11. [PMID: 30737185 PMCID: PMC6436931 DOI: 10.1016/j.molcel.2018.12.023] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/02/2018] [Accepted: 12/21/2018] [Indexed: 01/19/2023]
Abstract
Cleavage and polyadenylation factor (CPF/CPSF) is a multi-protein complex essential for formation of eukaryotic mRNA 3' ends. CPF cleaves pre-mRNAs at a specific site and adds a poly(A) tail. The cleavage reaction defines the 3' end of the mature mRNA, and thus the activity of the endonuclease is highly regulated. Here, we show that reconstitution of specific pre-mRNA cleavage with recombinant yeast proteins requires incorporation of the Ysh1 endonuclease into an eight-subunit "CPFcore" complex. Cleavage also requires the accessory cleavage factors IA and IB, which bind substrate pre-mRNAs and CPF, likely facilitating assembly of an active complex. Using X-ray crystallography, electron microscopy, and mass spectrometry, we determine the structure of Ysh1 bound to Mpe1 and the arrangement of subunits within CPFcore. Together, our data suggest that the active mRNA 3' end processing machinery is a dynamic assembly that is licensed to cleave only when all protein factors come together at the polyadenylation site.
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Affiliation(s)
- Chris H Hill
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | | | - Ana Casañal
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Peter Kubík
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Sarah Maslen
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Ottilie von Loeffelholz
- Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Illkirch, Université de Strasbourg, Strasbourg, France; Centre National de la Recherche Scientifique UMR 7104, Illkirch, Université de Strasbourg, Strasbourg, France; INSERM U964, Illkirch, Université de Strasbourg, Strasbourg, France
| | - Mathias Girbig
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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129
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The Core and Holoenzyme Forms of RNA Polymerase from Mycobacterium smegmatis. J Bacteriol 2019; 201:JB.00583-18. [PMID: 30478083 DOI: 10.1128/jb.00583-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/20/2018] [Indexed: 12/25/2022] Open
Abstract
Bacterial RNA polymerase (RNAP) is essential for gene expression and as such is a valid drug target. Hence, it is imperative to know its structure and dynamics. Here, we present two as-yet-unreported forms of Mycobacterium smegmatis RNAP: core and holoenzyme containing σA but no other factors. Each form was detected by cryo-electron microscopy in two major conformations. Comparisons of these structures with known structures of other RNAPs reveal a high degree of conformational flexibility of the mycobacterial enzyme and confirm that region 1.1 of σA is directed into the primary channel of RNAP. Taken together, we describe the conformational changes of unrestrained mycobacterial RNAP.IMPORTANCE We describe here three-dimensional structures of core and holoenzyme forms of mycobacterial RNA polymerase (RNAP) solved by cryo-electron microscopy. These structures fill the thus-far-empty spots in the gallery of the pivotal forms of mycobacterial RNAP and illuminate the extent of conformational dynamics of this enzyme. The presented findings may facilitate future designs of antimycobacterial drugs targeting RNAP.
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130
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Chang C, Young LN, Morris KL, von Bülow S, Schöneberg J, Yamamoto-Imoto H, Oe Y, Yamamoto K, Nakamura S, Stjepanovic G, Hummer G, Yoshimori T, Hurley JH. Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics. Mol Cell 2019; 73:339-353.e6. [PMID: 30581147 PMCID: PMC6450660 DOI: 10.1016/j.molcel.2018.10.035] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 09/15/2018] [Accepted: 10/19/2018] [Indexed: 12/11/2022]
Abstract
Membrane targeting of the BECN1-containing class III PI 3-kinase (PI3KC3) complexes is pivotal to the regulation of autophagy. The interaction of PI3KC3 complex II and its ubiquitously expressed inhibitor, Rubicon, was mapped to the first β sheet of the BECN1 BARA domain and the UVRAG BARA2 domain by hydrogen-deuterium exchange and cryo-EM. These data suggest that the BARA β sheet 1 unfolds to directly engage the membrane. This mechanism was confirmed using protein engineering, giant unilamellar vesicle assays, and molecular simulations. Using this mechanism, a BECN1 β sheet-1 derived peptide activates both PI3KC3 complexes I and II, while HIV-1 Nef inhibits complex II. These data reveal how BECN1 switches on and off PI3KC3 binding to membranes. The observations explain how PI3KC3 inhibition by Rubicon, activation by autophagy-inducing BECN1 peptides, and inhibition by HIV-1 Nef are mediated by the switchable ability of the BECN1 BARA domain to partially unfold and insert into membranes.
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Affiliation(s)
- Chunmei Chang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lindsey N Young
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kyle L Morris
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt/M, Germany
| | - Johannes Schöneberg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Hitomi Yamamoto-Imoto
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Yukako Oe
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Kentaro Yamamoto
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Shuhei Nakamura
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Goran Stjepanovic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt/M, Germany; Institute of Biophysics, Goethe University, 60438 Frankfurt/M, Germany
| | - Tamotsu Yoshimori
- Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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131
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Chen J, Noble AJ, Kang JY, Darst SA. Eliminating effects of particle adsorption to the air/water interface in single-particle cryo-electron microscopy: Bacterial RNA polymerase and CHAPSO. J Struct Biol X 2019; 1:100005. [PMID: 32285040 PMCID: PMC7153306 DOI: 10.1016/j.yjsbx.2019.100005] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 01/19/2019] [Accepted: 01/25/2019] [Indexed: 01/08/2023] Open
Abstract
Preferred particle orientation presents a major challenge for many single particle cryo-electron microscopy (cryo-EM) samples. Orientation bias limits the angular information used to generate three-dimensional maps and thus affects the reliability and interpretability of the structural models. The primary cause of preferred orientation is presumed to be due to adsorption of the particles at the air/water interface during cryo-EM grid preparation. To ameliorate this problem, detergents are often added to cryo-EM samples to alter the properties of the air/water interface. We have found that many bacterial transcription complexes suffer severe orientation bias when examined by cryo-EM. The addition of non-ionic detergents, such as NP-40, does not remove the orientation bias but the Zwitter-ionic detergent CHAPSO significantly broadens the particle orientation distributions, yielding isotropically uniform maps. We used cryo-electron tomography to examine the particle distribution within the ice layer of cryo-EM grid preparations of Escherichia coli 6S RNA/RNA polymerase holoenzyme particles. In the absence of CHAPSO, essentially all of the particles are located at the ice surfaces. CHAPSO at the critical micelle concentration eliminates particle absorption at the air/water interface and allows particles to randomly orient in the vitreous ice layer. We find that CHAPSO eliminates orientation bias for a wide range of bacterial transcription complexes containing E. coli or Mycobacterium tuberculosis RNA polymerases. Findings of this study confirm the presumed basis for how detergents can help remove orientation bias in cryo-EM samples and establishes CHAPSO as a useful tool to facilitate cryo-EM studies of bacterial transcription complexes.
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Affiliation(s)
- James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Alex J. Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Jin Young Kang
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065, USA
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132
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Patel AB, Louder RK, Greber BJ, Grünberg S, Luo J, Fang J, Liu Y, Ranish J, Hahn S, Nogales E. Structure of human TFIID and mechanism of TBP loading onto promoter DNA. Science 2018; 362:eaau8872. [PMID: 30442764 PMCID: PMC6446905 DOI: 10.1126/science.aau8872] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/06/2018] [Indexed: 12/22/2022]
Abstract
The general transcription factor IID (TFIID) is a critical component of the eukaryotic transcription preinitiation complex (PIC) and is responsible for recognizing the core promoter DNA and initiating PIC assembly. We used cryo-electron microscopy, chemical cross-linking mass spectrometry, and biochemical reconstitution to determine the complete molecular architecture of TFIID and define the conformational landscape of TFIID in the process of TATA box-binding protein (TBP) loading onto promoter DNA. Our structural analysis revealed five structural states of TFIID in the presence of TFIIA and promoter DNA, showing that the initial binding of TFIID to the downstream promoter positions the upstream DNA and facilitates scanning of TBP for a TATA box and the subsequent engagement of the promoter. Our findings provide a mechanistic model for the specific loading of TBP by TFIID onto the promoter.
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Affiliation(s)
- Avinash B Patel
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Robert K Louder
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Basil J Greber
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA 94720, USA
| | - Sebastian Grünberg
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Jie Fang
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Yutong Liu
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
| | - Jeff Ranish
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Steve Hahn
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Eva Nogales
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA.
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
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133
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Stella S, Mesa P, Thomsen J, Paul B, Alcón P, Jensen SB, Saligram B, Moses ME, Hatzakis NS, Montoya G. Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity. Cell 2018; 175:1856-1871.e21. [PMID: 30503205 DOI: 10.1016/j.cell.2018.10.045] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/27/2018] [Accepted: 10/22/2018] [Indexed: 02/07/2023]
Abstract
Cas12a, also known as Cpf1, is a type V-A CRISPR-Cas RNA-guided endonuclease that is used for genome editing based on its ability to generate specific dsDNA breaks. Here, we show cryo-EM structures of intermediates of the cleavage reaction, thus visualizing three protein regions that sense the crRNA-DNA hybrid assembly triggering the catalytic activation of Cas12a. Single-molecule FRET provides the thermodynamics and kinetics of the conformational activation leading to phosphodiester bond hydrolysis. These findings illustrate why Cas12a cuts its target DNA and unleashes unspecific cleavage activity, degrading ssDNA molecules after activation. In addition, we show that other crRNAs are able to displace the R-loop inside the protein after target DNA cleavage, terminating indiscriminate ssDNA degradation. We propose a model whereby the conformational activation of the enzyme results in indiscriminate ssDNA cleavage. The displacement of the R-loop by a new crRNA molecule will reset Cas12a specificity, targeting new DNAs.
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Affiliation(s)
- Stefano Stella
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Pablo Mesa
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Johannes Thomsen
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Bijoya Paul
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Pablo Alcón
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Simon B Jensen
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Bhargav Saligram
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Matias E Moses
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Nikos S Hatzakis
- Department of Chemistry & Nanoscience Centre, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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134
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Advances in image processing for single-particle analysis by electron cryomicroscopy and challenges ahead. Curr Opin Struct Biol 2018; 52:127-145. [PMID: 30509756 DOI: 10.1016/j.sbi.2018.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/26/2018] [Accepted: 11/17/2018] [Indexed: 12/20/2022]
Abstract
Electron cryomicroscopy (cryoEM) is essential for the study and functional understanding of non-crystalline macromolecules such as proteins. These molecules cannot be imaged using X-ray crystallography or other popular methods. CryoEM has been successfully used to visualize macromolecular complexes such as ribosomes, viruses, and ion channels. Determination of structural models of these at various conformational states leads to insight on how these molecules function. Recent advances in imaging technology have given cryoEM a scientific rebirth. As a result of these technological advances image processing and analysis have yielded molecular structures at atomic resolution. Nevertheless there continue to be challenges in image processing, and in this article we will touch on the most essential in order to derive an accurate three-dimensional model from noisy projection images. Traditional approaches, such as k-means clustering for class averaging, will be provided as background. We will then highlight new approaches for each image processing subproblem, including a 3D reconstruction method for asymmetric molecules using just two projection images and deep learning algorithms for automated particle picking.
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135
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Herzik MA, Fraser JS, Lander GC. A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality. Structure 2018; 27:344-358.e3. [PMID: 30449687 DOI: 10.1016/j.str.2018.10.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/17/2018] [Accepted: 10/10/2018] [Indexed: 02/06/2023]
Abstract
There does not currently exist a standardized indicator of how well cryo-EM-derived models represent the density from which they were generated. We present a straightforward methodology that utilizes freely available tools to generate a suite of independent models and to evaluate their convergence in an EM density. These analyses provide both a quantitative and qualitative assessment of the precision of the models and their representation of the density, respectively, while concurrently providing a platform for assessing both global and local EM map quality. We further use standardized datasets to provide an expected deviation within a suite of models refined against EM maps reported to be at 5 Å resolution or better. Associating multiple atomic models with a deposited EM map provides a rapid and accessible reporter of convergence, a strong indicator of highly resolved molecular detail, and is an important step toward an FSC-independent assessment of map and model quality.
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Affiliation(s)
- Mark A Herzik
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James S Fraser
- Department of Bioengineering and Therapeutic Science and California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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136
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Zivanov J, Nakane T, Forsberg BO, Kimanius D, Hagen WJ, Lindahl E, Scheres SH. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 2018; 7:42166. [PMID: 30412051 PMCID: PMC6250425 DOI: 10.7554/elife.42166] [Citation(s) in RCA: 3226] [Impact Index Per Article: 537.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/06/2018] [Indexed: 12/28/2022] Open
Abstract
Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2–0.7 Å compared to previous RELION versions.
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Affiliation(s)
- Jasenko Zivanov
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Takanori Nakane
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Björn O Forsberg
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Dari Kimanius
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Wim Jh Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Cryo-Electron Microscopy Service Platform, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden.,Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
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137
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Noble AJ, Wei H, Dandey VP, Zhang Z, Tan YZ, Potter CS, Carragher B. Reducing effects of particle adsorption to the air-water interface in cryo-EM. Nat Methods 2018; 15:793-795. [PMID: 30250056 PMCID: PMC6168394 DOI: 10.1038/s41592-018-0139-3] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/25/2018] [Indexed: 12/31/2022]
Abstract
Most protein particles prepared in vitreous ice for single-particle cryo-electron microscopy (cryo-EM) are adsorbed to air-water or substrate-water interfaces, which can cause the particles to adopt preferred orientations. By using a rapid plunge-freezing robot and nanowire grids, we were able to reduce some of the deleterious effects of the air-water interface by decreasing the dwell time of particles in thin liquid films. We demonstrated this by using single-particle cryo-EM and cryo-electron tomography (cryo-ET) to examine hemagglutinin, insulin receptor complex, and apoferritin.
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Affiliation(s)
- Alex J Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Hui Wei
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Venkata P Dandey
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Zhening Zhang
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Yong Zi Tan
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Clinton S Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
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138
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Boyd CM, Bubeck D. Advances in cryoEM and its impact on β-pore forming proteins. Curr Opin Struct Biol 2018; 52:41-49. [PMID: 30125772 PMCID: PMC6302071 DOI: 10.1016/j.sbi.2018.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 07/20/2018] [Accepted: 07/23/2018] [Indexed: 01/04/2023]
Abstract
Deployed by both hosts and pathogens, β-pore-forming proteins (β-PFPs) rupture membranes and lyse target cells. Soluble protein monomers oligomerize on the lipid bilayer where they undergo dramatic structural rearrangements, resulting in a transmembrane β-barrel pore. Advances in electron cryo-microscopy (cryoEM) sample preparation, image detection, and computational algorithms have led to a number of recent structures that reveal a molecular mechanism of pore formation in atomic detail.
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Affiliation(s)
- Courtney M Boyd
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Doryen Bubeck
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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139
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Sgro GG, Costa TRD. Cryo-EM Grid Preparation of Membrane Protein Samples for Single Particle Analysis. Front Mol Biosci 2018; 5:74. [PMID: 30131964 PMCID: PMC6090150 DOI: 10.3389/fmolb.2018.00074] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/10/2018] [Indexed: 11/26/2022] Open
Abstract
Recent advances in cryo-electron microscopy (cryo-EM) have made it possible to solve structures of biological macromolecules at near atomic resolution. Development of more stable microscopes, improved direct electron detectors and faster software for image processing has enabled structural solution of not only large macromolecular (megadalton range) complexes but also small (~60 kDa) proteins. As a result of the widespread use of the technique, we have also witnessed new developments of techniques for cryo-EM grid preparation of membrane protein samples. This includes new types of solubilization strategies that better stabilize these protein complexes and the development of new grid supports with proven efficacy in reducing the motion of the molecules during electron beam exposure. Here, we discuss the practicalities and recent challenges of membrane protein sample preparation and vitrification, as well as grid support and foil treatment in the context of the structure determination of protein complexes by single particle cryo-EM.
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Affiliation(s)
- Germán G. Sgro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago R. D. Costa
- Department of Life Sciences, Imperial College London, MRC Centre for Molecular Microbiology and Infection, London, United Kingdom
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140
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Noble AJ, Dandey VP, Wei H, Brasch J, Chase J, Acharya P, Tan YZ, Zhang Z, Kim LY, Scapin G, Rapp M, Eng ET, Rice WJ, Cheng A, Negro CJ, Shapiro L, Kwong PD, Jeruzalmi D, des Georges A, Potter CS, Carragher B. Routine single particle CryoEM sample and grid characterization by tomography. eLife 2018; 7:e34257. [PMID: 29809143 PMCID: PMC5999397 DOI: 10.7554/elife.34257] [Citation(s) in RCA: 181] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/17/2018] [Indexed: 12/11/2022] Open
Abstract
Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment.
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Affiliation(s)
- Alex J Noble
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Venkata P Dandey
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Hui Wei
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Julia Brasch
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUnited States
| | - Jillian Chase
- Department of Chemistry and BiochemistryCity College of New YorkNew YorkUnited States
- Program in BiochemistryThe Graduate Center of the City University of New YorkNew YorkUnited States
| | - Priyamvada Acharya
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Vaccine Research CenterNational Institute of Allergy and Infectious Diseases, National Institutes of HealthMarylandUnited States
| | - Yong Zi Tan
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUnited States
| | - Zhening Zhang
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Laura Y Kim
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Giovanna Scapin
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Department of Structural Chemistry and Chemical BiotechnologyMerck & Co., IncNew JerseyUnited States
| | - Micah Rapp
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUnited States
| | - Edward T Eng
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - William J Rice
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Anchi Cheng
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Carl J Negro
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUnited States
| | - Peter D Kwong
- Vaccine Research CenterNational Institute of Allergy and Infectious Diseases, National Institutes of HealthMarylandUnited States
| | - David Jeruzalmi
- Department of Chemistry and BiochemistryCity College of New YorkNew YorkUnited States
- Program in BiochemistryThe Graduate Center of the City University of New YorkNew YorkUnited States
- Program in BiologyThe Graduate Center of the City University of New YorkNew YorkUnited States
- Program in ChemistryThe Graduate Center of the City University of New YorkNew YorkUnited States
| | - Amedee des Georges
- Department of Chemistry and BiochemistryCity College of New YorkNew YorkUnited States
- Program in BiochemistryThe Graduate Center of the City University of New YorkNew YorkUnited States
- Program in ChemistryThe Graduate Center of the City University of New YorkNew YorkUnited States
- Advanced Science Research CenterThe Graduate Center of the City University of New YorkNew YorkUnited States
| | - Clinton S Potter
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUnited States
| | - Bridget Carragher
- National Resource for Automated Molecular MicroscopySimons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkUnited States
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141
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Abstract
It has become clear that the standard cartoon, in which macromolecular particles prepared for electron cryo-microscopy are shown to be surrounded completely by vitreous ice, often is not accurate. In particular, the standard picture does not include the fact that diffusion to the air-water interface, followed by adsorption and possibly denaturation, can occur on the time scale that normally is required to make thin specimens. The extensive literature on interaction of proteins with the air-water interface suggests that many proteins can bind to the interface, either directly or indirectly via a sacrificial layer of already-denatured protein. In the process, the particles of interest can, in some cases, become preferentially oriented, and in other cases they can be damaged and/or aggregated at the surface. Thus, although a number of methods and recipes have evolved for dealing with protein complexes that prove to be difficult, making good cryo-grids can still be a major challenge for each new type of specimen. Recognition that the air-water interface is a very dangerous place to be has inspired work on some novel approaches for preparing cryo-grids. At the moment, two of the most promising ones appear to be: (1) thin and vitrify the specimen much faster than is done currently or (2) immobilize the particles onto a structure-friendly support film so that they cannot diffuse to the air-water interface.
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Affiliation(s)
- Robert M Glaeser
- Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94705
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142
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Improving the efficiency of cryo-EM. Nat Methods 2017. [DOI: 10.1038/nmeth.4523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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143
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Boland A, Chang L, Barford D. The potential of cryo-electron microscopy for structure-based drug design. Essays Biochem 2017; 61:543-560. [PMID: 29118099 DOI: 10.1042/ebc20170032] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 12/17/2022]
Abstract
Structure-based drug design plays a central role in therapeutic development. Until recently, protein crystallography and NMR have dominated experimental approaches to obtain structural information of biological molecules. However, in recent years rapid technical developments in single particle cryo-electron microscopy (cryo-EM) have enabled the determination to near-atomic resolution of macromolecules ranging from large multi-subunit molecular machines to proteins as small as 64 kDa. These advances have revolutionized structural biology by hugely expanding both the range of macromolecules whose structures can be determined, and by providing a description of macromolecular dynamics. Cryo-EM is now poised to similarly transform the discipline of structure-based drug discovery. This article reviews the potential of cryo-EM for drug discovery with reference to protein ligand complex structures determined using this technique.
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Affiliation(s)
- Andreas Boland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Leifu Chang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - David Barford
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K.
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144
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Casañal A, Kumar A, Hill CH, Easter AD, Emsley P, Degliesposti G, Gordiyenko Y, Santhanam B, Wolf J, Wiederhold K, Dornan GL, Skehel M, Robinson CV, Passmore LA. Architecture of eukaryotic mRNA 3'-end processing machinery. Science 2017; 358:1056-1059. [PMID: 29074584 PMCID: PMC5788269 DOI: 10.1126/science.aao6535] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/12/2017] [Indexed: 12/31/2022]
Abstract
Newly transcribed eukaryotic precursor messenger RNAs (pre-mRNAs) are processed at their 3' ends by the ~1-megadalton multiprotein cleavage and polyadenylation factor (CPF). CPF cleaves pre-mRNAs, adds a polyadenylate tail, and triggers transcription termination, but it is unclear how its various enzymes are coordinated and assembled. Here, we show that the nuclease, polymerase, and phosphatase activities of yeast CPF are organized into three modules. Using electron cryomicroscopy, we determined a 3.5-angstrom-resolution structure of the ~200-kilodalton polymerase module. This revealed four β propellers, in an assembly markedly similar to those of other protein complexes that bind nucleic acid. Combined with in vitro reconstitution experiments, our data show that the polymerase module brings together factors required for specific and efficient polyadenylation, to help coordinate mRNA 3'-end processing.
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Affiliation(s)
- Ana Casañal
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Chris H Hill
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Yuliya Gordiyenko
- MRC Laboratory of Molecular Biology, Cambridge, UK.,Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | | | - Jana Wolf
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
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