51
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Vollmer B, Pražák V, Vasishtan D, Jefferys EE, Hernandez-Duran A, Vallbracht M, Klupp BG, Mettenleiter TC, Backovic M, Rey FA, Topf M, Grünewald K. The prefusion structure of herpes simplex virus glycoprotein B. SCIENCE ADVANCES 2020; 6:eabc1726. [PMID: 32978151 PMCID: PMC7518877 DOI: 10.1126/sciadv.abc1726] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/12/2020] [Indexed: 05/03/2023]
Abstract
Cell entry of enveloped viruses requires specialized viral proteins that mediate fusion with the host membrane by substantial structural rearrangements from a metastable pre- to a stable postfusion conformation. This metastability renders the herpes simplex virus 1 (HSV-1) fusion glycoprotein B (gB) highly unstable such that it readily converts into the postfusion form, thereby precluding structural elucidation of the pharmacologically relevant prefusion conformation. By identification of conserved sequence signatures and molecular dynamics simulations, we devised a mutation that stabilized this form. Functionally locking gB allowed the structural determination of its membrane-embedded prefusion conformation at sub-nanometer resolution and enabled the unambiguous fit of all ectodomains. The resulting pseudo-atomic model reveals a notable conservation of conformational domain rearrangements during fusion between HSV-1 gB and the vesicular stomatitis virus glycoprotein G, despite their very distant phylogeny. In combination with our comparative sequence-structure analysis, these findings suggest common fusogenic domain rearrangements in all class III viral fusion proteins.
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Affiliation(s)
- B Vollmer
- Oxford Particle Imaging Centre, Department of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, Oxford, UK
- Centre for Structural Systems Biology, Heinrich-Pette-Institut, Leibniz-Institut für Experimentelle Virologie, Hamburg, Germany
| | - V Pražák
- Oxford Particle Imaging Centre, Department of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, Oxford, UK
| | - D Vasishtan
- Oxford Particle Imaging Centre, Department of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, Oxford, UK
| | - E E Jefferys
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - M Vallbracht
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Insel Riems, Germany
| | - B G Klupp
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Insel Riems, Germany
| | - T C Mettenleiter
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Insel Riems, Germany
| | - M Backovic
- Institut Pasteur, Structural Virology Unit, Department of Virology, Paris, France
| | - F A Rey
- Institut Pasteur, Structural Virology Unit, Department of Virology, Paris, France
| | - M Topf
- Institute of Structural and Molecular Biology, Birkbeck, London, UK
| | - K Grünewald
- Oxford Particle Imaging Centre, Department of Structural Biology, Wellcome Centre Human Genetics, University of Oxford, Oxford, UK.
- Centre for Structural Systems Biology, Heinrich-Pette-Institut, Leibniz-Institut für Experimentelle Virologie, Hamburg, Germany
- Department of Chemistry, MIN Faculty, Universität Hamburg, Hamburg, Germany
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52
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The Architecture of Talin1 Reveals an Autoinhibition Mechanism. Cell 2020; 179:120-131.e13. [PMID: 31539492 PMCID: PMC6856716 DOI: 10.1016/j.cell.2019.08.034] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 04/04/2019] [Accepted: 08/16/2019] [Indexed: 12/15/2022]
Abstract
Focal adhesions (FAs) are protein machineries essential for cell adhesion, migration, and differentiation. Talin is an integrin-activating and tension-sensing FA component directly connecting integrins in the plasma membrane with the actomyosin cytoskeleton. To understand how talin function is regulated, we determined a cryoelectron microscopy (cryo-EM) structure of full-length talin1 revealing a two-way mode of autoinhibition. The actin-binding rod domains fold into a 15-nm globular arrangement that is interlocked by the integrin-binding FERM head. In turn, the rod domains R9 and R12 shield access of the FERM domain to integrin and the phospholipid PIP2 at the membrane. This mechanism likely ensures synchronous inhibition of integrin, membrane, and cytoskeleton binding. We also demonstrate that compacted talin1 reversibly unfolds to an ∼60-nm string-like conformation, revealing interaction sites for vinculin and actin. Our data explain how fast switching between active and inactive conformations of talin could regulate FA turnover, a process critical for cell adhesion and signaling. The structure of the autoinhibited human full-length talin1 was analyzed by cryo-EM Talin1 reversibly changes between a 15-nm closed and a ∼60-nm open conformation Rod R9/R12 and FERM domains synchronously shield membrane and cytoskeleton binding F-Actin and vinculin binding to talin is regulated by the opening of talin
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53
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Hirschi M, Lu WT, Santiago-Frangos A, Wilkinson R, Golden SM, Davidson AR, Lander GC, Wiedenheft B. AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex. Nat Commun 2020; 11:2730. [PMID: 32483187 PMCID: PMC7264359 DOI: 10.1038/s41467-020-16512-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/07/2020] [Indexed: 11/09/2022] Open
Abstract
Bacteria have evolved sophisticated adaptive immune systems, called CRISPR-Cas, that provide sequence-specific protection against phage infection. In turn, phages have evolved a broad spectrum of anti-CRISPRs that suppress these immune systems. Here we report structures of anti-CRISPR protein IF9 (AcrIF9) in complex with the type I-F CRISPR RNA-guided surveillance complex (Csy). In addition to sterically blocking the hybridization of complementary dsDNA to the CRISPR RNA, our results show that AcrIF9 binding also promotes non-sequence-specific engagement with dsDNA, potentially sequestering the complex from target DNA. These findings highlight the versatility of anti-CRISPR mechanisms utilized by phages to suppress CRISPR-mediated immune systems.
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Affiliation(s)
- Marscha Hirschi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92121, USA
| | - Wang-Ting Lu
- Department of Molecular Genetics, and Department of Biochemistry, University of Toronto, 661 University Avenue, Room 1634, Toronto, ON, M5G 1M1, Canada
| | - Andrew Santiago-Frangos
- Department of Microbiology and Immunology, Montana State University, 1156 South 11th Avenue, Bozeman, MT, 59717, USA
| | - Royce Wilkinson
- Department of Microbiology and Immunology, Montana State University, 1156 South 11th Avenue, Bozeman, MT, 59717, USA
| | - Sarah M Golden
- Department of Microbiology and Immunology, Montana State University, 1156 South 11th Avenue, Bozeman, MT, 59717, USA
| | - Alan R Davidson
- Department of Molecular Genetics, and Department of Biochemistry, University of Toronto, 661 University Avenue, Room 1634, Toronto, ON, M5G 1M1, Canada.
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92121, USA.
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, 1156 South 11th Avenue, Bozeman, MT, 59717, USA.
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54
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Jin W, Wang J, Liu CP, Wang HW, Xu RM. Structural Basis for pri-miRNA Recognition by Drosha. Mol Cell 2020; 78:423-433.e5. [DOI: 10.1016/j.molcel.2020.02.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/13/2020] [Accepted: 02/27/2020] [Indexed: 12/22/2022]
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55
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Liu F, Zhang Z, Levit A, Levring J, Touhara KK, Shoichet BK, Chen J. Structural identification of a hotspot on CFTR for potentiation. Science 2020; 364:1184-1188. [PMID: 31221859 DOI: 10.1126/science.aaw7611] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/31/2019] [Indexed: 12/18/2022]
Abstract
Cystic fibrosis is a fatal disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR). Two main categories of drugs are being developed: correctors that improve folding of CFTR and potentiators that recover the function of CFTR. Here, we report two cryo-electron microscopy structures of human CFTR in complex with potentiators: one with the U.S. Food and Drug Administration (FDA)-approved drug ivacaftor at 3.3-angstrom resolution and the other with an investigational drug, GLPG1837, at 3.2-angstrom resolution. These two drugs, although chemically dissimilar, bind to the same site within the transmembrane region. Mutagenesis suggests that in both cases, hydrogen bonds provided by the protein are important for drug recognition. The molecular details of how ivacaftor and GLPG1837 interact with CFTR may facilitate structure-based optimization of therapeutic compounds.
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Affiliation(s)
- Fangyu Liu
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY 10065, USA.,Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, NY 10065, USA
| | - Zhe Zhang
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY 10065, USA
| | - Anat Levit
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jesper Levring
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY 10065, USA
| | - Kouki K Touhara
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jue Chen
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, NY 10065, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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56
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Beckers M, Palmer CM, Sachse C. Confidence maps: statistical inference of cryo-EM maps. Acta Crystallogr D Struct Biol 2020; 76:332-339. [PMID: 32254057 PMCID: PMC7137106 DOI: 10.1107/s2059798320002995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/03/2020] [Indexed: 11/11/2022] Open
Abstract
Confidence maps provide complementary information for interpreting cryo-EM densities as they indicate statistical significance with respect to background noise. They can be thresholded by specifying the expected false-discovery rate (FDR), and the displayed volume shows the parts of the map that have the corresponding level of significance. Here, the basic statistical concepts of confidence maps are reviewed and practical guidance is provided for their interpretation and usage inside the CCP-EM suite. Limitations of the approach are discussed and extensions towards other error criteria such as the family-wise error rate are presented. The observed map features can be rendered at a common isosurface threshold, which is particularly beneficial for the interpretation of weak and noisy densities. In the current article, a practical guide is provided to the recommended usage of confidence maps.
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Affiliation(s)
- Maximilian Beckers
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Colin M. Palmer
- Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom
| | - Carsten Sachse
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons 3/Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52425 Jülich, Germany
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57
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Zehni M, Donati L, Soubies E, Zhao ZJ, Unser M. Joint Angular Refinement and Reconstruction for Single-Particle Cryo-EM. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2020; 29:6151-6163. [PMID: 32248108 DOI: 10.1109/tip.2020.2984313] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-particle cryo-electron microscopy (cryo-EM) reconstructs the three-dimensional (3D) structure of biomolecules from a large set of 2D projection images with random and unknown orientations. A crucial step in the single-particle cryo-EM pipeline is 3D refinement, which resolves a highresolution 3D structure from an initial approximate volume by refining the estimation of the orientation of each projection. In this work, we propose a new approach that refines the projection angles on the continuum. We formulate the optimization problem over the density map and the orientations jointly. The density map is updated using the efficient alternating-direction method of multipliers, while the orientations are updated through a semicoordinate- wise gradient descent for which we provide an explicit derivation of the gradient. Our method eliminates the requirement for a fine discretization of the orientation space and does away with the classical but computationally expensive templatematching step. Numerical results demonstrate the feasibility and performance of our approach compared to several baselines.
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58
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de la Rosa-Trevín JM, Hernández Viga PA, Otón J, Lindahl E. Development of basic building blocks for cryo-EM: the emcore and emvis software libraries. Acta Crystallogr D Struct Biol 2020; 76:350-356. [PMID: 32254059 PMCID: PMC7137102 DOI: 10.1107/s2059798320003769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 03/13/2020] [Indexed: 11/10/2022] Open
Abstract
Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled. Moreover, data processing has become more accessible to many experimental groups, with computations that used to last for many days at supercomputing facilities now being performed in hours on personal workstations. All of these advances, together with the rapid expansion of the community, continue to pose challenges and new demands on the software-development side. In this article, the development of emcore and emvis, two basic software libraries for image manipulation and data visualization in cryo-EM, is presented. The main goal is to provide basic functionality organized in modular components that other developers can reuse to implement new algorithms or build graphical applications. An additional aim is to showcase the importance of following established practices in software engineering, with the hope that this could be a first step towards a more standardized way of developing and distributing software in the field.
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Affiliation(s)
| | | | - Joaquín Otón
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
- Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
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59
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Arnold FM, Weber MS, Gonda I, Gallenito MJ, Adenau S, Egloff P, Zimmermann I, Hutter CAJ, Hürlimann LM, Peters EE, Piel J, Meloni G, Medalia O, Seeger MA. The ABC exporter IrtAB imports and reduces mycobacterial siderophores. Nature 2020; 580:413-417. [PMID: 32296173 PMCID: PMC7170716 DOI: 10.1038/s41586-020-2136-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 02/24/2020] [Indexed: 12/17/2022]
Abstract
Intracellular replication of the deadly pathogen Mycobacterium tuberculosis relies on the production of small organic molecules called siderophores to scavenge iron from host proteins1. M. tuberculosis produces two classes of siderophores, lipid-bound mycobactin and soluble carboxymycobactin2, 3. Functional studies revealed that iron-loaded carboxymycobactin is imported into the cytoplasm by the ABC transporter IrtAB4, which features an additional cytoplasmic siderophore interaction domain (SID)5. However, IrtAB’s predicted ABC exporter fold seemingly contradicts its import function. Here, we show that membrane-reconstituted IrtAB is sufficient to import mycobactins, which are then reduced by the SID to facilitate iron release. Structure determination by X-ray crystallography and cryo-EM confirms IrtAB’s ABC exporter fold, but also reveals structural peculiarities at the transmembrane region of IrtAB resulting in a partially collapsed inward-facing substrate binding cavity. The SID is positioned in close proximity to the inner membrane leaflet, which allows the reduction of membrane-inserted mycobactin. Enzymatic ATPase activity and in vivo growth assays show that IrtAB prefers mycobactin over carboxymycobactin as its substrate. Our study provides insights into an unusual ABC exporter that evolved as highly specialized siderophore import machinery in mycobacteria.
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Affiliation(s)
- Fabian M Arnold
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Miriam S Weber
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Imre Gonda
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Marc J Gallenito
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA
| | - Sophia Adenau
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Pascal Egloff
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics, Zurich, Switzerland
| | - Iwan Zimmermann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.,Linkster Therapeutics, Zurich, Switzerland
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Lea M Hürlimann
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Eike E Peters
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Gabriele Meloni
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, TX, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
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60
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Huang W, Masureel M, Qu Q, Janetzko J, Inoue A, Kato HE, Robertson MJ, Nguyen KC, Glenn JS, Skiniotis G, Kobilka BK. Structure of the neurotensin receptor 1 in complex with β-arrestin 1. Nature 2020; 579:303-308. [PMID: 31945771 PMCID: PMC7100716 DOI: 10.1038/s41586-020-1953-1] [Citation(s) in RCA: 217] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 01/08/2020] [Indexed: 01/14/2023]
Abstract
Arrestin proteins bind to active, phosphorylated G-protein-coupled receptors (GPCRs), thereby preventing G-protein coupling, triggering receptor internalization and affecting various downstream signalling pathways1,2. Although there is a wealth of structural information detailing the interactions between GPCRs and G proteins, less is known about how arrestins engage GPCRs. Here we report a cryo-electron microscopy structure of full-length human neurotensin receptor 1 (NTSR1) in complex with truncated human β-arrestin 1 (βarr1(ΔCT)). We find that phosphorylation of NTSR1 is critical for the formation of a stable complex with βarr1(ΔCT), and identify phosphorylated sites in both the third intracellular loop and the C terminus that may promote this interaction. In addition, we observe a phosphatidylinositol-4,5-bisphosphate molecule forming a bridge between the membrane side of NTSR1 transmembrane segments 1 and 4 and the C-lobe of arrestin. Compared with a structure of a rhodopsin-arrestin-1 complex, in our structure arrestin is rotated by approximately 85° relative to the receptor. These findings highlight both conserved aspects and plasticity among arrestin-receptor interactions.
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Affiliation(s)
- Weijiao Huang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthieu Masureel
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Qianhui Qu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - John Janetzko
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Hideaki E Kato
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Komaba Institute for Science, The University of Tokyo, Tokyo, Japan
| | - Michael J Robertson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Khanh C Nguyen
- Departments of Medicine and Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Jeffrey S Glenn
- Departments of Medicine and Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Photon Science, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
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61
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Kepsutlu B, Wycisk V, Achazi K, Kapishnikov S, Pérez-Berná AJ, Guttmann P, Cossmer A, Pereiro E, Ewers H, Ballauff M, Schneider G, McNally JG. Cells Undergo Major Changes in the Quantity of Cytoplasmic Organelles after Uptake of Gold Nanoparticles with Biologically Relevant Surface Coatings. ACS NANO 2020; 14:2248-2264. [PMID: 31951375 DOI: 10.1021/acsnano.9b09264] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Here, we use cryo soft X-ray tomography (cryo-SXT), which delivers 3D ultrastructural volumes of intact cells without chemical fixation or staining, to gain insight about nanoparticle uptake for nanomedicine. We initially used dendritic polyglycerol sulfate (dPGS) with potential diagnostic and therapeutic applications in inflammation. Although dPGS-coated gold nanoparticle (dPGS-AuNP) uptake followed a conventional endocytic/degradative pathway in human lung epithelial cell lines (A549), with cryo-SXT, we detected ∼5% of dPGS-AuNPs in the cytoplasm, a level undetectable by confocal light microscopy. We also observed ∼5% of dPGS-AuNPs in a rarely identified subcellular site, namely, lipid droplets, which are important for cellular energy metabolism. Finally, we also found substantial changes in the quantity of cytoplasmic organelles upon dPGS-AuNP uptake over the 1-6 h incubation period; the number of small vesicles and mitochondria significantly increased, and the number of multivesicular bodies and the number and volume of lipid droplets significantly decreased. Although nearly all organelle numbers at 6 h were still significantly different from controls, most appeared to be returning to normal levels. To test for generality, we also examined cells after uptake of gold nanoparticles coated with a different agent, polyethylenimine (PEI), used for nucleic acid delivery. PEI nanoparticles did not enter lipid droplets, but they induced similar, albeit less pronounced, changes in the quantity of cytoplasmic organelles. We confirmed these changes in organelle quantities for both nanoparticle coatings by confocal fluorescence microscopy. We suggest this cytoplasmic remodeling could reflect a more common cellular response to coated gold nanoparticle uptake.
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Affiliation(s)
- Burcu Kepsutlu
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
| | - Virginia Wycisk
- Organische Chemie, Institut für Chemie und Biochemie , Freie Universität Berlin , Takustrasse 3 , D-14195 Berlin , Germany
| | - Katharina Achazi
- Organische Chemie, Institut für Chemie und Biochemie , Freie Universität Berlin , Takustrasse 3 , D-14195 Berlin , Germany
| | - Sergey Kapishnikov
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
| | - Ana Joaquina Pérez-Berná
- ALBA Synchrotron Light Source , MISTRAL Beamline Experiments Division , Cerdanyola del Vallès , 08290 Barcelona , Spain
| | - Peter Guttmann
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
| | - Antje Cossmer
- Division 1.1 - Inorganic Trace Analysis , Federal Institute for Materials Research and Testing (BAM) , Richard-Willstätter-Str. 11 , 12489 Berlin , Germany
| | - Eva Pereiro
- ALBA Synchrotron Light Source , MISTRAL Beamline Experiments Division , Cerdanyola del Vallès , 08290 Barcelona , Spain
| | - Helge Ewers
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
- Institute of Chemistry and Biochemisty, Department of Biology, Chemistry and Pharmacy , Freie Universität Berlin , Thielallee 63 , 14195 Berlin , Germany
| | - Matthias Ballauff
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
- Institute of Physics , Humboldt Universität zu Berlin , Newtonstraße 15 , 12489 Berlin , Germany
| | - Gerd Schneider
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
- Institute of Physics , Humboldt Universität zu Berlin , Newtonstraße 15 , 12489 Berlin , Germany
| | - James G McNally
- Helmholtz Zentrum Berlin für Materialien und Energie GmbH , Wilhelm-Conrad-Röntgen Campus, Albert-Einstein-Str. 15 , 12489 Berlin , Germany
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62
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Wang J, Song X, Zhang D, Chen X, Li X, Sun Y, Li C, Song Y, Ding Y, Ren R, Harrington EH, Hu LA, Zhong W, Xu C, Huang X, Wang HW, Ma Y. Cryo-EM structures of PAC1 receptor reveal ligand binding mechanism. Cell Res 2020; 30:436-445. [PMID: 32047270 PMCID: PMC7196072 DOI: 10.1038/s41422-020-0280-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/20/2020] [Indexed: 12/24/2022] Open
Abstract
The pituitary adenylate cyclase-activating polypeptide type I receptor (PAC1R) belongs to the secretin receptor family and is widely distributed in the central neural system and peripheral organs. Abnormal activation of the receptor mediates trigeminovascular activation and sensitization, which is highly related to migraine, making PAC1R a potential therapeutic target. Elucidation of PAC1R activation mechanism would benefit discovery of therapeutic drugs for neuronal disorders. PAC1R activity is governed by pituitary adenylate cyclase-activating polypeptide (PACAP), known as a major vasodilator neuropeptide, and maxadilan, a native peptide from the sand fly, which is also capable of activating the receptor with similar potency. These peptide ligands have divergent sequences yet initiate convergent PAC1R activity. It is of interest to understand the mechanism of PAC1R ligand recognition and receptor activity regulation through structural biology. Here we report two near-atomic resolution cryo-EM structures of PAC1R activated by PACAP38 or maxadilan, providing structural insights into two distinct ligand binding modes. The structures illustrate flexibility of the extracellular domain (ECD) for ligands with distinct conformations, where ECD accommodates ligands in different orientations while extracellular loop 1 (ECL1) protrudes to further anchor the ligand bound in the orthosteric site. By structure-guided molecular modeling and mutagenesis, we tested residues in the ligand-binding pockets and identified clusters of residues that are critical for receptor activity. The structures reported here for the first time elucidate the mechanism of specificity and flexibility of ligand recognition and binding for PAC1R, and provide insights toward the design of therapeutic molecules targeting PAC1R.
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Affiliation(s)
- Jia Wang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xianqiang Song
- Amgen Asia R&D Center, Amgen Research, Bldg. 2, 13th Floor, No. 4560 Jinke Road, Shanghai, 201210, China
| | - Dandan Zhang
- Amgen Asia R&D Center, Amgen Research, Bldg. 2, 13th Floor, No. 4560 Jinke Road, Shanghai, 201210, China
| | - Xiaoqing Chen
- Amgen Asia R&D Center, Amgen Research, Bldg. 2, 13th Floor, No. 4560 Jinke Road, Shanghai, 201210, China
| | - Xun Li
- Amgen Asia R&D Center, Amgen Research, Bldg. 2, 13th Floor, No. 4560 Jinke Road, Shanghai, 201210, China
| | - Yaping Sun
- Amgen Asia R&D Center, Amgen Research, Bldg. 2, 13th Floor, No. 4560 Jinke Road, Shanghai, 201210, China
| | - Cui Li
- Amgen Asia R&D Center, Amgen Research, Bldg. 2, 13th Floor, No. 4560 Jinke Road, Shanghai, 201210, China
| | - Yunpeng Song
- Amgen Asia R&D Center, Amgen Research, Bldg. 2, 13th Floor, No. 4560 Jinke Road, Shanghai, 201210, China
| | - Yao Ding
- Amgen Asia R&D Center, Amgen Research, Bldg. 2, 13th Floor, No. 4560 Jinke Road, Shanghai, 201210, China
| | - Ruobing Ren
- School of Life and Health Sciences, Kobilka Institute of Innovative Drug Discovery, The Chinese University of Hong Kong, Tu H.L. Building (Research Building B) R705, Longxiang Road 2001, Longgang district, Shenzhen, 518172, Guangdong, China
| | - Essa Hu Harrington
- Hybrid Modality Engineering, Therapeutic Discovery, Amgen Research, One Amgen Center Dr., Thousand Oaks, CA, 91320, USA
| | - Liaoyuan A Hu
- Amgen Asia R&D Center, Amgen Research, Bldg. 2, 13th Floor, No. 4560 Jinke Road, Shanghai, 201210, China
| | - Wenge Zhong
- Amgen Asia R&D Center, Amgen Research, Bldg. 2, 13th Floor, No. 4560 Jinke Road, Shanghai, 201210, China
| | - Cen Xu
- Department of Neuroscience, Amgen Research, One Amgen Center Dr., Thousand Oaks, CA, 91320, USA
| | - Xin Huang
- Molecular Engineering, Therapeutic Discovery, Amgen Research, 360 Binney Street, Cambridge, MA, 02142, USA
| | - Hong-Wei Wang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Yingli Ma
- Amgen Asia R&D Center, Amgen Research, Bldg. 2, 13th Floor, No. 4560 Jinke Road, Shanghai, 201210, China.
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63
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Wang Z, Hu W, Zheng H. Pathogenic siderophore ABC importer YbtPQ adopts a surprising fold of exporter. SCIENCE ADVANCES 2020; 6:eaay7997. [PMID: 32076651 PMCID: PMC7002159 DOI: 10.1126/sciadv.aay7997] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/22/2019] [Indexed: 05/05/2023]
Abstract
To fight for essential metal ions, human pathogens secrete virulence-associated siderophores and retake the metal-chelated siderophores through a subfamily of adenosine triphosphate (ATP)-binding cassette (ABC) importer, whose molecular mechanisms are completely unknown. We have determined multiple structures of the yersiniabactin importer YbtPQ from uropathogenic Escherichia coli (UPEC) at inward-open conformation in both apo and substrate-bound states by cryo-electron microscopy. YbtPQ does not adopt any known fold of ABC importers but surprisingly adopts the fold of type IV ABC exporters. To our knowledge, it is the first time an exporter fold of ABC importer has been reported. We have also observed two unique features in YbtPQ: unwinding of a transmembrane helix in YbtP upon substrate release and tightly associated nucleotide-binding domains without bound nucleotides. Together, our study suggests that siderophore ABC importers have a distinct transport mechanism and should be classified as a separate subfamily of ABC importers.
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64
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Heymann JB. Protocols for Processing and Interpreting cryoEM Data Using Bsoft: A Case Study of the Retinal Adhesion Protein, Retinoschisin. Bio Protoc 2020; 10:e3491. [PMID: 33654723 DOI: 10.21769/bioprotoc.3491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 11/26/2019] [Accepted: 12/02/2019] [Indexed: 11/02/2022] Open
Abstract
The goal of cryoEM is to determine the structures of biomolecules from electron micrographs. In many cases the processing is straightforward and can be handled with routine protocols. In other cases, the properties and behavior of the specimen require adaptions to properly interpret the data. Here I describe the protocols for examining the higher order assemblies of the retinal adhesion protein, retinoschisin (RS1), using the Bsoft package. The protocols for micrograph preprocessing, 2D classification and 3D alignment and reconstruction follow the usual patterns for the majority of cryoEM specimens. The interpretation of the results is specific to the branched network of RS1 filaments. The 2D class averages are used to determine the relative positions of the RS1 molecules, thus defining the interacting interfaces in the network. The major interface of the linear filament is then further examined by reconstructing the "unit cell" and fitting the molecular models.
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Affiliation(s)
- J Bernard Heymann
- Laboratory for Structural Biology Research, NIAMS, NIH, Bethesda, MD 20892, USA
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65
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Bodrug T, Wilson-Kubalek EM, Nithianantham S, Thompson AF, Alfieri A, Gaska I, Major J, Debs G, Inagaki S, Gutierrez P, Gheber L, McKenney RJ, Sindelar CV, Milligan R, Stumpff J, Rosenfeld SS, Forth ST, Al-Bassam J. The kinesin-5 tail domain directly modulates the mechanochemical cycle of the motor domain for anti-parallel microtubule sliding. eLife 2020; 9:e51131. [PMID: 31958056 PMCID: PMC7015671 DOI: 10.7554/elife.51131] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/16/2020] [Indexed: 12/29/2022] Open
Abstract
Kinesin-5 motors organize mitotic spindles by sliding apart microtubules. They are homotetramers with dimeric motor and tail domains at both ends of a bipolar minifilament. Here, we describe a regulatory mechanism involving direct binding between tail and motor domains and its fundamental role in microtubule sliding. Kinesin-5 tails decrease microtubule-stimulated ATP-hydrolysis by specifically engaging motor domains in the nucleotide-free or ADP states. Cryo-EM reveals that tail binding stabilizes an open motor domain ATP-active site. Full-length motors undergo slow motility and cluster together along microtubules, while tail-deleted motors exhibit rapid motility without clustering. The tail is critical for motors to zipper together two microtubules by generating substantial sliding forces. The tail is essential for mitotic spindle localization, which becomes severely reduced in tail-deleted motors. Our studies suggest a revised microtubule-sliding model, in which kinesin-5 tails stabilize motor domains in the microtubule-bound state by slowing ATP-binding, resulting in high-force production at both homotetramer ends.
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Affiliation(s)
- Tatyana Bodrug
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
| | - Elizabeth M Wilson-Kubalek
- Department of Integrative Structural and Computational BiologyScripps Research InstituteLa JollaUnited States
| | - Stanley Nithianantham
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
| | - Alex F Thompson
- Department of Molecular Physiology and BiophysicsUniversity of VermontBurlingtonUnited States
| | - April Alfieri
- Department of Biological SciencesRensselaer Polytechnic InstituteTroyUnited States
| | - Ignas Gaska
- Department of Biological SciencesRensselaer Polytechnic InstituteTroyUnited States
| | - Jennifer Major
- Department of Cancer BiologyLerner Research Institute, Cleveland ClinicLorainUnited States
- Department of PharmacologyMayo ClinicJacksonvilleUnited States
| | - Garrett Debs
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States
| | - Sayaka Inagaki
- Department of PharmacologyMayo ClinicJacksonvilleUnited States
| | - Pedro Gutierrez
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
| | - Larisa Gheber
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and TechnologyBen-Gurion University of the NegevNegevIsrael
| | - Richard J McKenney
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
| | | | - Ronald Milligan
- Department of Integrative Structural and Computational BiologyScripps Research InstituteLa JollaUnited States
| | - Jason Stumpff
- Department of Molecular Physiology and BiophysicsUniversity of VermontBurlingtonUnited States
| | - Steven S Rosenfeld
- Department of Cancer BiologyLerner Research Institute, Cleveland ClinicLorainUnited States
- Department of PharmacologyMayo ClinicJacksonvilleUnited States
| | - Scott T Forth
- Department of Biological SciencesRensselaer Polytechnic InstituteTroyUnited States
| | - Jawdat Al-Bassam
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
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66
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Staus DP, Hu H, Robertson MJ, Kleinhenz ALW, Wingler LM, Capel WD, Latorraca NR, Lefkowitz RJ, Skiniotis G. Structure of the M2 muscarinic receptor-β-arrestin complex in a lipid nanodisc. Nature 2020; 579:297-302. [PMID: 31945772 PMCID: PMC7367492 DOI: 10.1038/s41586-020-1954-0] [Citation(s) in RCA: 200] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/07/2020] [Indexed: 02/07/2023]
Abstract
Following agonist activation, G protein-coupled receptors (GPCRs) recruit β-arrestin, which desensitizes heterotrimeric G protein signaling and promotes receptor endocytosis1. Additionally, β-arrestin directly regulates many cell signaling pathways that can induce cellular responses distinct from that of G proteins2. Here we present a cryo-electron microscopy (cryoEM) structure of β-arrestin1 (βarr1) in complex with muscarinic acetylcholine-2-receptor (M2R) reconstituted in lipid nanodiscs. The M2R-βarr1 structure shows a multimodal network of flexible interactions, including binding of the βarr1 N-domain to phosphorylated receptor residues and βarr1 finger loop insertion into the M2R seven-transmembrane bundle, which adopts a conformation similar to that in the M2R-heterotrimeric Go protein structure3. Moreover, the cryoEM map reveals that the βarr1 C-domain edge engages the lipid bilayer. Through atomistic simulations, biophysical, biochemical, and cellular assays, we show that the C-edge is critical for stable complex formation, βarr1 recruitment, receptor internalization, and desensitization of G protein activation. Taken together, these data suggest the cooperative interactions of β-arrestin with both the receptor and phospholipid bilayer contribute to its functional versatility.
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Affiliation(s)
- Dean P Staus
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.,Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, USA
| | - Hongli Hu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,School of Life and Health Sciences, Kobilka Institute of Innovative Drug Discovery, The Chinese University of Hong Kong, Shenzhen, China
| | - Michael J Robertson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alissa L W Kleinhenz
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.,Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, USA.,School of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Laura M Wingler
- Department of Medicine, Duke University Medical Center, Durham, NC, USA.,Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, USA
| | - William D Capel
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Naomi R Latorraca
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Computer Science, Stanford University, Stanford, CA, USA.,Biophysics Program, Stanford University, Stanford, CA, USA
| | - Robert J Lefkowitz
- Department of Medicine, Duke University Medical Center, Durham, NC, USA. .,Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, USA. .,Department of Biochemistry, Duke University Medical Center, Durham, NC, USA.
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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67
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Ng CT, Gan L. Investigating eukaryotic cells with cryo-ET. Mol Biol Cell 2020; 31:87-100. [PMID: 31935172 PMCID: PMC6960407 DOI: 10.1091/mbc.e18-05-0329] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 01/06/2023] Open
Abstract
The interior of eukaryotic cells is mysterious. How do the large communities of macromolecular machines interact with each other? How do the structures and positions of these nanoscopic entities respond to new stimuli? Questions like these can now be answered with the help of a method called electron cryotomography (cryo-ET). Cryo-ET will ultimately reveal the inner workings of a cell at the protein, secondary structure, and perhaps even side-chain levels. Combined with genetic or pharmacological perturbation, cryo-ET will allow us to answer previously unimaginable questions, such as how structure, biochemistry, and forces are related in situ. Because it bridges structural biology and cell biology, cryo-ET is indispensable for structural cell biology-the study of the 3-D macromolecular structure of cells. Here we discuss some of the key ideas, strategies, auxiliary techniques, and innovations that an aspiring structural cell biologist will consider when planning to ask bold questions.
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Affiliation(s)
- Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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68
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Pye VE, Rosa A, Bertelli C, Struwe WB, Maslen SL, Corey R, Liko I, Hassall M, Mattiuzzo G, Ballandras-Colas A, Nans A, Takeuchi Y, Stansfeld PJ, Skehel JM, Robinson CV, Pizzato M, Cherepanov P. A bipartite structural organization defines the SERINC family of HIV-1 restriction factors. Nat Struct Mol Biol 2020; 27:78-83. [PMID: 31907454 PMCID: PMC6956856 DOI: 10.1038/s41594-019-0357-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/26/2019] [Indexed: 12/14/2022]
Abstract
The human integral membrane protein SERINC5 potently restricts HIV-1 infectivity and sensitizes the virus to antibody-mediated neutralization. Here, using cryo-EM, we determine the structures of human SERINC5 and its orthologue from Drosophila melanogaster at subnanometer and near-atomic resolution, respectively. The structures reveal a novel fold comprised of ten transmembrane helices organized into two subdomains and bisected by a long diagonal helix. A lipid binding groove and clusters of conserved residues highlight potential functional sites. A structure-based mutagenesis scan identified surface-exposed regions and the interface between the subdomains of SERINC5 as critical for HIV-1-restriction activity. The same regions are also important for viral sensitization to neutralizing antibodies, directly linking the antiviral activity of SERINC5 with remodeling of the HIV-1 envelope glycoprotein.
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Affiliation(s)
- Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London, UK
| | - Annachiara Rosa
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London, UK
| | - Cinzia Bertelli
- Department of Cellular, Computational and Integrative Biology, University of Trento, Povo, Italy
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, UK
| | - Sarah L Maslen
- Biological Mass Spectrometry and Proteomics Laboratory, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Robin Corey
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Idlir Liko
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, UK
| | - Mark Hassall
- National Institute for Biological Standards and Control, Hertfordshire, UK
| | - Giada Mattiuzzo
- National Institute for Biological Standards and Control, Hertfordshire, UK
| | | | - Andrea Nans
- Structural Biology Science Technology Platform, Francis Crick Institute, London, UK
| | - Yasuhiro Takeuchi
- National Institute for Biological Standards and Control, Hertfordshire, UK
- UCL Division of Infection and Immunity, The Rayne Building, London, UK
| | - Phillip J Stansfeld
- Department of Biochemistry, University of Oxford, Oxford, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Warwick, UK
| | - J Mark Skehel
- Biological Mass Spectrometry and Proteomics Laboratory, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, UK
| | - Massimo Pizzato
- Department of Cellular, Computational and Integrative Biology, University of Trento, Povo, Italy.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, Francis Crick Institute, London, UK.
- Department of Infectious Disease, Imperial College London, St Mary's Campus, Norfolk Place, London, UK.
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69
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Lawson CL, Berman HM, Chiu W. Evolving data standards for cryo-EM structures. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:014701. [PMID: 32002441 PMCID: PMC6980868 DOI: 10.1063/1.5138589] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/07/2020] [Indexed: 05/04/2023]
Abstract
Electron cryo-microscopy (cryo-EM) is increasingly being used to determine 3D structures of a broad spectrum of biological specimens from molecules to cells. Anticipating this progress in the early 2000s, an international collaboration of scientists with expertise in both cryo-EM and structure data archiving was established (EMDataResource, previously known as EMDataBank). The major goals of the collaboration have been twofold: to develop the necessary infrastructure for archiving cryo-EM-derived density maps and models, and to promote development of cryo-EM structure validation standards. We describe how cryo-EM data archiving and validation have been developed and jointly coordinated for the Electron Microscopy Data Bank and Protein Data Bank archives over the past two decades, as well as the impact of evolving technology on data standards. Just as for X-ray crystallography and nuclear magnetic resonance, engaging the scientific community via workshops and challenging activities has played a central role in developing recommendations and requirements for the cryo-EM structure data archives.
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Affiliation(s)
- Catherine L. Lawson
- Institute for Quantitative Biomedicine and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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70
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Kaiser CJO, Peters C, Schmid PWN, Stavropoulou M, Zou J, Dahiya V, Mymrikov EV, Rockel B, Asami S, Haslbeck M, Rappsilber J, Reif B, Zacharias M, Buchner J, Weinkauf S. The structure and oxidation of the eye lens chaperone αA-crystallin. Nat Struct Mol Biol 2019; 26:1141-1150. [PMID: 31792453 PMCID: PMC7115824 DOI: 10.1038/s41594-019-0332-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 10/10/2019] [Indexed: 11/08/2022]
Abstract
The small heat shock protein αA-crystallin is a molecular chaperone important for the optical properties of the vertebrate eye lens. It forms heterogeneous oligomeric ensembles. We determined the structures of human αA-crystallin oligomers by combining cryo-electron microscopy, cross-linking/mass spectrometry, NMR spectroscopy and molecular modeling. The different oligomers can be interconverted by the addition or subtraction of tetramers, leading to mainly 12-, 16- and 20-meric assemblies in which interactions between N-terminal regions are important. Cross-dimer domain-swapping of the C-terminal region is a determinant of αA-crystallin heterogeneity. Human αA-crystallin contains two cysteines, which can form an intramolecular disulfide in vivo. Oxidation in vitro requires conformational changes and oligomer dissociation. The oxidized oligomers, which are larger than reduced αA-crystallin and destabilized against unfolding, are active chaperones and can transfer the disulfide to destabilized substrate proteins. The insight into the structure and function of αA-crystallin provides a basis for understanding its role in the eye lens.
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Affiliation(s)
- Christoph J O Kaiser
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Carsten Peters
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Philipp W N Schmid
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Maria Stavropoulou
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Juan Zou
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Vinay Dahiya
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Evgeny V Mymrikov
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
- Institute for Biochemistry and Molecular Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Beate Rockel
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Sam Asami
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Haslbeck
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Bernd Reif
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin Zacharias
- Center for Integrated Protein Science Munich at the Physics Department, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany.
| | - Sevil Weinkauf
- Center for Integrated Protein Science Munich at the Department Chemie, Technische Universität München, Garching, Germany.
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71
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Choi W, Clemente N, Sun W, Du J, Lü W. The structures and gating mechanism of human calcium homeostasis modulator 2. Nature 2019; 576:163-167. [PMID: 31776515 DOI: 10.1038/s41586-019-1781-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 10/08/2019] [Indexed: 12/14/2022]
Abstract
Calcium homeostasis modulators (CALHMs) are voltage-gated, Ca2+-inhibited nonselective ion channels that act as major ATP release channels, and have important roles in gustatory signalling and neuronal toxicity1-3. Dysfunction of CALHMs has previously been linked to neurological disorders1. Here we present cryo-electron microscopy structures of the human CALHM2 channel in the Ca2+-free active or open state and in the ruthenium red (RUR)-bound inhibited state, at resolutions up to 2.7 Å. Our work shows that purified CALHM2 channels form both gap junctions and undecameric hemichannels. The protomer shows a mirrored arrangement of the transmembrane domains (helices S1-S4) relative to other channels with a similar topology, such as connexins, innexins and volume-regulated anion channels4-8. Upon binding to RUR, we observed a contracted pore with notable conformational changes of the pore-lining helix S1, which swings nearly 60° towards the pore axis from a vertical to a lifted position. We propose a two-section gating mechanism in which the S1 helix coarsely adjusts, and the N-terminal helix fine-tunes, the pore size. We identified a RUR-binding site near helix S1 that may stabilize this helix in the lifted conformation, giving rise to channel inhibition. Our work elaborates on the principles of CALHM2 channel architecture and symmetry, and the mechanism that underlies channel inhibition.
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Affiliation(s)
| | | | - Weinan Sun
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA.,Janelia Research Campus, Ashburn, VA, USA
| | - Juan Du
- Van Andel Institute, Grand Rapids, MI, USA.
| | - Wei Lü
- Van Andel Institute, Grand Rapids, MI, USA.
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72
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Subramanian S, Maurer AC, Bator CM, Makhov AM, Conway JF, Turner KB, Marden JH, Vandenberghe LH, Hafenstein SL. Filling Adeno-Associated Virus Capsids: Estimating Success by Cryo-Electron Microscopy. Hum Gene Ther 2019; 30:1449-1460. [PMID: 31530236 DOI: 10.1089/hum.2019.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Adeno-associated viruses (AAVs) have been employed successfully as gene therapy vectors in treating various genetic diseases for almost two decades. However, transgene packaging is usually imperfect, and developing a rapid and accurate method for measuring the proportion of DNA encapsidation is an important step for improving the downstream process of large scale vector production. In this study, we used two-dimensional class averages and three-dimensional classes, intermediate outputs in the single particle cryo-electron microscopy (cryo-EM) image reconstruction pipeline, to determine the proportion of DNA-packaged and empty capsid populations. Two different preparations of AAV3 were analyzed to estimate the minimum number of particles required to be sampled by cryo-EM in order for robust calculation of the proportion of the full versus empty capsids in any given sample. Cost analysis applied to the minimum amount of data required for a valid ratio suggests that cryo-EM is an effective approach to analyze vector preparations.
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Affiliation(s)
- Suriyasri Subramanian
- Department of Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania
| | - Anna C Maurer
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Massachusetts Eye and Ear, Boston, Massachusetts.,Department of Ophthalmology, Harvard Medical School, Ocular Genomics Institute, Boston, Massachusetts.,The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Carol M Bator
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania
| | - Alexander M Makhov
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - James F Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kevin B Turner
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - James H Marden
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania.,Department of Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Luk H Vandenberghe
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Massachusetts Eye and Ear, Boston, Massachusetts.,Department of Ophthalmology, Harvard Medical School, Ocular Genomics Institute, Boston, Massachusetts.,The Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Susan L Hafenstein
- Department of Medicine, The Pennsylvania State University College of Medicine, Hershey, Pennsylvania.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania
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73
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Cui Y, Zhang Y, Zhou K, Sun J, Zhou ZH. Conservative transcription in three steps visualized in a double-stranded RNA virus. Nat Struct Mol Biol 2019; 26:1023-1034. [PMID: 31695188 DOI: 10.1038/s41594-019-0320-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/19/2019] [Indexed: 01/28/2023]
Abstract
Endogenous RNA transcription characterizes double-stranded RNA (dsRNA) viruses in the Reoviridae, a family that is exemplified by its simple, single-shelled member cytoplasmic polyhedrosis virus (CPV). Because of the lack of in situ structures of the intermediate stages of RNA-dependent RNA polymerase (RdRp) during transcription, it is poorly understood how RdRp detects environmental cues and internal transcriptional states to initiate and coordinate repeated cycles of transcript production inside the capsid. Here, we captured five high-resolution (2.8-3.5 Å) RdRp-RNA in situ structures-representing quiescent, initiation, early elongation, elongation and abortive states-under seven experimental conditions of CPV. We observed the 'Y'-form initial RNA fork in the initiation state and the complete transcription bubble in the elongation state. These structures reveal that de novo RNA transcription involves three major conformational changes during state transitions. Our results support an ouroboros model for endogenous conservative transcription in dsRNA viruses.
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Affiliation(s)
- Yanxiang Cui
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yinong Zhang
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.,Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Kang Zhou
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jingchen Sun
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA. .,Subtropical Sericulture and Mulberry Resources Protection and Safety Engineering Research Center, Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.
| | - Z Hong Zhou
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA. .,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
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74
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Vanden Broeck A, Lotz C, Ortiz J, Lamour V. Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Nat Commun 2019; 10:4935. [PMID: 31666516 PMCID: PMC6821735 DOI: 10.1038/s41467-019-12914-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022] Open
Abstract
DNA gyrase is an essential enzyme involved in the homeostatic control of DNA supercoiling and the target of successful antibacterial compounds. Despite extensive studies, a detailed architecture of the full-length DNA gyrase from the model organism E. coli is still missing. Herein, we report the complete structure of the E. coli DNA gyrase nucleoprotein complex trapped by the antibiotic gepotidacin, using phase-plate single-particle cryo-electron microscopy. Our data unveil the structural and spatial organization of the functional domains, their connections and the position of the conserved GyrA-box motif. The deconvolution of two states of the DNA-binding/cleavage domain provides a better understanding of the allosteric movements of the enzyme complex. The local atomic resolution in the DNA-bound area reaching up to 3.0 Å enables the identification of the antibiotic density. Altogether, this study paves the way for the cryo-EM determination of gyrase complexes with antibiotics and opens perspectives for targeting conformational intermediates. Bacterial DNA gyrase is the only type II DNA topoisomerase capable of introducing negative supercoils into DNA and is of interest as a drug target. Here the authors present the cryo-EM structure of the complete E. coli DNA gyrase bound to a 180 bp double-stranded DNA and the antibiotic gepotidacin, which reveals the connections between the functional domains and their spatial organization.
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Affiliation(s)
- Arnaud Vanden Broeck
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Christophe Lotz
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Julio Ortiz
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France.,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Valérie Lamour
- Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France. .,Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France. .,Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France. .,Université de Strasbourg, Illkirch, France. .,Hôpitaux Universitaires de Strasbourg, 1 Place de l'Hôpital, 67091, Strasbourg Cedex, France.
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75
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Maluenda D, Majtner T, Horvath P, Vilas JL, Jiménez-Moreno A, Mota J, Ramírez-Aportela E, Sánchez-García R, Conesa P, del Caño L, Rancel Y, Fonseca Y, Martínez M, Sharov G, García C, Strelak D, Melero R, Marabini R, Carazo JM, Sorzano COS. Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion. Acta Crystallogr D Struct Biol 2019; 75:882-894. [PMID: 31588920 PMCID: PMC6778851 DOI: 10.1107/s2059798319011860] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/28/2019] [Indexed: 01/18/2023] Open
Abstract
Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 Å resolution β-galactosidase data set.
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Affiliation(s)
- D. Maluenda
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - T. Majtner
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - P. Horvath
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - J. L. Vilas
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - A. Jiménez-Moreno
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - J. Mota
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | | | - R. Sánchez-García
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - P. Conesa
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - L. del Caño
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - Y. Rancel
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - Y. Fonseca
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - M. Martínez
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - G. Sharov
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, England
| | | | - D. Strelak
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - R. Melero
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - R. Marabini
- Universidad Autónoma de Madrid, Madrid, Spain
| | - J. M. Carazo
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
| | - C. O. S. Sorzano
- National Center for Biotechnology (CSIC), 28049 Cantoblanco, Madrid, Spain
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76
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The cryo-EM structure of the acid activatable pore-forming immune effector Macrophage-expressed gene 1. Nat Commun 2019; 10:4288. [PMID: 31537793 PMCID: PMC6753088 DOI: 10.1038/s41467-019-12279-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/28/2019] [Indexed: 11/08/2022] Open
Abstract
Macrophage-expressed gene 1 (MPEG1/Perforin-2) is a perforin-like protein that functions within the phagolysosome to damage engulfed microbes. MPEG1 is thought to form pores in target membranes, however, its mode of action remains unknown. We use cryo-Electron Microscopy (cryo-EM) to determine the 2.4 Å structure of a hexadecameric assembly of MPEG1 that displays the expected features of a soluble prepore complex. We further discover that MPEG1 prepore-like assemblies can be induced to perforate membranes through acidification, such as would occur within maturing phagolysosomes. We next solve the 3.6 Å cryo-EM structure of MPEG1 in complex with liposomes. These data reveal that a multi-vesicular body of 12 kDa (MVB12)-associated β-prism (MABP) domain binds membranes such that the pore-forming machinery of MPEG1 is oriented away from the bound membrane. This unexpected mechanism of membrane interaction suggests that MPEG1 remains bound to the phagolysosome membrane while simultaneously forming pores in engulfed bacterial targets. Macrophage-expressed gene 1 (MPEG1) functions within the phagolysosome to damage engulfed microbes, presumably via forming pores in target membranes. In order to provide insights into the mechanism of MPEG1 function and membrane binding, the authors present structures of hexadecameric MPEG1 prepores both in solution and in complex with liposomes.
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77
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Svidritskiy E, Demo G, Loveland AB, Xu C, Korostelev AA. Extensive ribosome and RF2 rearrangements during translation termination. eLife 2019; 8:46850. [PMID: 31513010 PMCID: PMC6742477 DOI: 10.7554/elife.46850] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/28/2019] [Indexed: 12/31/2022] Open
Abstract
Protein synthesis ends when a ribosome reaches an mRNA stop codon. Release factors (RFs) decode the stop codon, hydrolyze peptidyl-tRNA to release the nascent protein, and then dissociate to allow ribosome recycling. To visualize termination by RF2, we resolved a cryo-EM ensemble of E. coli 70S•RF2 structures at up to 3.3 Å in a single sample. Five structures suggest a highly dynamic termination pathway. Upon peptidyl-tRNA hydrolysis, the CCA end of deacyl-tRNA departs from the peptidyl transferase center. The catalytic GGQ loop of RF2 is rearranged into a long β-hairpin that plugs the peptide tunnel, biasing a nascent protein toward the ribosome exit. Ribosomal intersubunit rotation destabilizes the catalytic RF2 domain on the 50S subunit and disassembles the central intersubunit bridge B2a, resulting in RF2 departure. Our structures visualize how local rearrangements and spontaneous inter-subunit rotation poise the newly-made protein and RF2 to dissociate in preparation for ribosome recycling.
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Affiliation(s)
- Egor Svidritskiy
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Gabriel Demo
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Anna B Loveland
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States
| | - Chen Xu
- Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
| | - Andrei A Korostelev
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, United States.,Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
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78
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Kwon E, Pathak D, Kim HU, Dahal P, Ha SC, Lee SS, Jeong H, Jeoung D, Chang HW, Jung HS, Kim DY. Structural insights into stressosome assembly. IUCRJ 2019; 6:938-947. [PMID: 31576226 PMCID: PMC6760441 DOI: 10.1107/s205225251900945x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/02/2019] [Indexed: 05/05/2023]
Abstract
The stressosome transduces environmental stress signals to SigB to upregulate SigB-dependent transcription, which is required for bacterial viability. The stressosome core is composed of RsbS and at least one of the RsbR paralogs. A previous cryo-electron microscopy (cryo-EM) structure of the RsbRA-RsbS complex determined under a D2 symmetry restraint showed that the stressosome core forms a pseudo-icosahedron consisting of 60 STAS domains of RsbRA and RsbS. However, it is still unclear how RsbS and one of the RsbR paralogs assemble into the stressosome. Here, an assembly model of the stressosome is presented based on the crystal structure of the RsbS icosahedron and cryo-EM structures of the RsbRA-RsbS complex determined under diverse symmetry restraints (nonsymmetric C1, dihedral D2 and icosahedral I envelopes). 60 monomers of the crystal structure of RsbS fitted well into the I-restrained cryo-EM structure determined at 4.1 Å resolution, even though the STAS domains in the I envelope were averaged. This indicates that RsbS and RsbRA share a highly conserved STAS fold. 22 protrusions observed in the C1 envelope, corresponding to dimers of the RsbRA N-domain, allowed the STAS domains of RsbRA and RsbS to be distinguished in the stressosome core. Based on these, the model of the stressosome core was reconstructed. The mutation of RsbRA residues at the binding interface in the model (R189A/Q191A) significantly reduced the interaction between RsbRA and RsbS. These results suggest that nonconserved residues in the conserved STAS folds between RsbS and RsbR paralogs determine stressosome assembly.
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Affiliation(s)
- Eunju Kwon
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Deepak Pathak
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Han-ul Kim
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Pawan Dahal
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Sung Chul Ha
- Pohang Accelerator Laboratory (PAL), Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Seung Sik Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Hyeongseop Jeong
- Center for Electron Microscopy Research, Korea Basic Science Institute, Ochang 28119, Republic of Korea
| | - Dooil Jeoung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
| | - Hyeun Wook Chang
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
| | - Hyun Suk Jung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, Gangwon 24341, Republic of Korea
- Correspondence e-mail: ,
| | - Dong Young Kim
- College of Pharmacy, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Republic of Korea
- Correspondence e-mail: ,
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79
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Early Scanning of Nascent Polypeptides inside the Ribosomal Tunnel by NAC. Mol Cell 2019; 75:996-1006.e8. [PMID: 31377116 DOI: 10.1016/j.molcel.2019.06.030] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 05/08/2019] [Accepted: 06/19/2019] [Indexed: 11/24/2022]
Abstract
Cotranslational processing of newly synthesized proteins is fundamental for correct protein maturation. Protein biogenesis factors are thought to bind nascent polypeptides not before they exit the ribosomal tunnel. Here, we identify a nascent chain recognition mechanism deep inside the ribosomal tunnel by an essential eukaryotic cytosolic chaperone. The nascent polypeptide-associated complex (NAC) inserts the N-terminal tail of its β subunit (N-βNAC) into the ribosomal tunnel to sense substrates directly upon synthesis close to the peptidyl-transferase center. N-βNAC escorts the growing polypeptide to the cytosol and relocates to an alternate binding site on the ribosomal surface. Using C. elegans as an in vivo model, we demonstrate that the tunnel-probing activity of NAC is essential for organismal viability and critical to regulate endoplasmic reticulum (ER) protein transport by controlling ribosome-Sec61 translocon interactions. Thus, eukaryotic protein maturation relies on the early sampling of nascent chains inside the ribosomal tunnel.
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80
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Walter JD, Sawicka M, Dutzler R. Cryo-EM structures and functional characterization of murine Slc26a9 reveal mechanism of uncoupled chloride transport. eLife 2019; 8:46986. [PMID: 31339488 PMCID: PMC6656431 DOI: 10.7554/elife.46986] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/21/2019] [Indexed: 12/14/2022] Open
Abstract
The epithelial anion transporter SLC26A9 contributes to airway surface hydration and gastric acid production. Colocalizing with CFTR, SLC26A9 has been proposed as a target for the treatment of cystic fibrosis. To provide molecular details of its transport mechanism, we present cryo-EM structures and a functional characterization of murine Slc26a9. These structures define the general architecture of eukaryotic SLC26 family members and reveal an unusual mode of oligomerization which relies predominantly on the cytosolic STAS domain. Our data illustrates conformational transitions of Slc26a9, supporting a rapid alternate-access mechanism which mediates uncoupled chloride transport with negligible bicarbonate or sulfate permeability. The characterization of structure-guided mutants illuminates the properties of the ion transport path, including a selective anion binding site located in the center of a mobile module within the transmembrane domain. This study thus provides a structural foundation for the understanding of the entire SLC26 family and potentially facilitates their therapeutic exploitation. Many processes in the human body are regulated by chloride and other charged particles (known as ions) moving in and out of cells. Each cell is surrounded by a membrane barrier, which prevents ions from entering or exiting. Therefore, to control the levels of ions inside the cell, specific proteins in the membrane act as channels or transporters to provide routes for the ions to pass through the membrane. Channel proteins form pores that, when open, allow a steady stream of ions to pass through the membrane. Transporter proteins, on the other hand, generally contain a pocket that is only accessible from one side of the membrane. When individual ions enter this pocket the transporter changes shape. This causes the entrance of the pocket to close and then re-open on the other side of the membrane. Inside the lung, an ion channel known as CFTR provides a route for chloride ions to move out of cells, which helps clear harmful material from the airways. Mutations affecting this protein cause the mucus lining the airways to become very sticky, leading to a severe disease known as cystic fibrosis. CFTR works together with another protein that is also found in the membrane, called SLC26A9. Previous studies have suggested that SLC26A9 also allows chloride ions to pass through the membrane. It was not clear, however, if SLC26A9 operates as an ion channel or a transporter protein, or how the protein is arranged in the membrane. Now, Walter, Sawicka and Dutzler combined two techniques known as cryo-electron microscopy and patch-clamp electrophysiology to reveal the detailed three-dimensional structure of the mouse version of SLC26A9, which is highly similar to the human form. The experiments found that mouse SLC26A9 proteins form pairs in the membrane referred to as homodimers, which arranged themselves in an unexpected way. Further investigation into the structure of these homodimers suggests that despite having many channel-like properties, SLC26A9 operates as a fast transporter, rather than a true channel. These findings help us understand the role of SLC26A9 and other similar proteins in the lung and other parts of the body. In the future it may be possible to develop drugs that target SLC26A9 to treat cystic fibrosis and other severe lung diseases.
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Affiliation(s)
- Justin D Walter
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Marta Sawicka
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Raimund Dutzler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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81
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Gao Y, Hu H, Ramachandran S, Erickson JW, Cerione RA, Skiniotis G. Structures of the Rhodopsin-Transducin Complex: Insights into G-Protein Activation. Mol Cell 2019; 75:781-790.e3. [PMID: 31300275 DOI: 10.1016/j.molcel.2019.06.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/16/2019] [Accepted: 06/04/2019] [Indexed: 12/31/2022]
Abstract
Rhodopsin (Rho), a prototypical G-protein-coupled receptor (GPCR) in vertebrate vision, activates the G-protein transducin (GT) by catalyzing GDP-GTP exchange on its α subunit (GαT). To elucidate the determinants of GT coupling and activation, we obtained cryo-EM structures of a fully functional, light-activated Rho-GT complex in the presence and absence of a G-protein-stabilizing nanobody. The structures illustrate how GT overcomes its low basal activity by engaging activated Rho in a conformation distinct from other GPCR-G-protein complexes. Moreover, the nanobody-free structures reveal native conformations of G-protein components and capture three distinct conformers showing the GαT helical domain (αHD) contacting the Gβγ subunits. These findings uncover the molecular underpinnings of G-protein activation by visual rhodopsin and shed new light on the role played by Gβγ during receptor-catalyzed nucleotide exchange.
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Affiliation(s)
- Yang Gao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Hongli Hu
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sekar Ramachandran
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jon W Erickson
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Richard A Cerione
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA.
| | - Georgios Skiniotis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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82
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Kežar A, Kavčič L, Polák M, Nováček J, Gutiérrez-Aguirre I, Žnidarič MT, Coll A, Stare K, Gruden K, Ravnikar M, Pahovnik D, Žagar E, Merzel F, Anderluh G, Podobnik M. Structural basis for the multitasking nature of the potato virus Y coat protein. SCIENCE ADVANCES 2019; 5:eaaw3808. [PMID: 31328164 PMCID: PMC6636993 DOI: 10.1126/sciadv.aaw3808] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/10/2019] [Indexed: 05/02/2023]
Abstract
Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl-terminal regions of the coat protein units and viral RNA. RNA-coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein's amino- and carboxyl-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus-like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications.
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Affiliation(s)
- Andreja Kežar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- Graduate School of Biomedicine, Medical Faculty, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Luka Kavčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Martin Polák
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Jiří Nováček
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, Brno 625 00, Czech Republic
| | - Ion Gutiérrez-Aguirre
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Katja Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- University of Nova Gorica, Vipavska cesta, 5000 Nova Gorica, Slovenia
| | - David Pahovnik
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Ema Žagar
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
- Corresponding author.
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83
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Wang J, Wang J, Hu M, Wu S, Qi J, Wang G, Han Z, Qi Y, Gao N, Wang HW, Zhou JM, Chai J. Ligand-triggered allosteric ADP release primes a plant NLR complex. Science 2019; 364:364/6435/eaav5868. [PMID: 30948526 DOI: 10.1126/science.aav5868] [Citation(s) in RCA: 259] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/13/2019] [Indexed: 12/16/2022]
Abstract
Pathogen recognition by nucleotide-binding (NB), leucine-rich repeat (LRR) receptors (NLRs) plays roles in plant immunity. The Xanthomonas campestris pv. campestris effector AvrAC uridylylates the Arabidopsis PBL2 kinase, and the latter (PBL2UMP) acts as a ligand to activate the NLR ZAR1 precomplexed with the RKS1 pseudokinase. Here we report the cryo-electron microscopy structures of ZAR1-RKS1 and ZAR1-RKS1-PBL2UMP in an inactive and intermediate state, respectively. The ZAR1LRR domain, compared with animal NLRLRR domains, is differently positioned to sequester ZAR1 in an inactive state. Recognition of PBL2UMP is exclusively through RKS1, which interacts with ZAR1LRR PBL2UMP binding stabilizes the RKS1 activation segment, which sterically blocks ZAR1 adenosine diphosphate (ADP) binding. This engenders a more flexible NB domain without conformational changes in the other ZAR1 domains. Our study provides a structural template for understanding plant NLRs.
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Affiliation(s)
- Jizong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jia Wang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Meijuan Hu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
| | - Shan Wu
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Jinfeng Qi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
| | - Guoxun Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
| | - Zhifu Han
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Yijun Qi
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Ning Gao
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China
| | - Hong-Wei Wang
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China.
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Academy of Seed Design, Chinese Academy of Sciences, 100101 Beijing, China.
| | - Jijie Chai
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, 100084 Beijing, China. .,Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany.,Institute of Biochemistry, University of Cologne, Zuelpicher Str. 47, 50674 Cologne, Germany
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84
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Cryo-EM structure of oxysterol-bound human Smoothened coupled to a heterotrimeric G i. Nature 2019; 571:279-283. [PMID: 31168089 DOI: 10.1038/s41586-019-1286-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/15/2019] [Indexed: 01/18/2023]
Abstract
The oncoprotein Smoothened (SMO), a G-protein-coupled receptor (GPCR) of the Frizzled-class (class-F), transduces the Hedgehog signal from the tumour suppressor Patched-1 (PTCH1) to the glioma-associated-oncogene (GLI) transcription factors, which activates the Hedgehog signalling pathway1,2. It has remained unknown how PTCH1 modulates SMO, how SMO is stimulated to form a complex with heterotrimeric G proteins and whether G-protein coupling contributes to the activation of GLI proteins3. Here we show that 24,25-epoxycholesterol, which we identify as an endogenous ligand of PTCH1, can stimulate Hedgehog signalling in cells and can trigger G-protein signalling via human SMO in vitro. We present a cryo-electron microscopy structure of human SMO bound to 24(S),25-epoxycholesterol and coupled to a heterotrimeric Gi protein. The structure reveals a ligand-binding site for 24(S),25-epoxycholesterol in the 7-transmembrane region, as well as a Gi-coupled activation mechanism of human SMO. Notably, the Gi protein presents a different arrangement from that of class-A GPCR-Gi complexes. Our work provides molecular insights into Hedgehog signal transduction and the activation of a class-F GPCR.
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85
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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: 86] [Impact Index Per Article: 17.2] [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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86
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Gan L, Ng CT, Chen C, Cai S. A collection of yeast cellular electron cryotomography data. Gigascience 2019; 8:giz077. [PMID: 31247098 PMCID: PMC6596884 DOI: 10.1093/gigascience/giz077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/09/2019] [Accepted: 06/10/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Cells are powered by a large set of macromolecular complexes, which work together in a crowded environment. The in situ mechanisms of these complexes are unclear because their 3D distribution, organization, and interactions are largely unknown. Electron cryotomography (cryo-ET) can address these knowledge gaps because it produces cryotomograms-3D images that reveal biological structure at ∼4-nm resolution. Cryo-ET uses no fixation, dehydration, staining, or plastic embedment, so cellular features are visualized in a life-like, frozen-hydrated state. To study chromatin and mitotic machinery in situ, we subjected yeast cells to genetic and chemical perturbations, cryosectioned them, and then imaged the cells by cryo-ET. FINDINGS Here we share >1,000 cryo-ET raw datasets of cryosectioned budding yeast Saccharomyces cerevisiaecollected as part of previously published studies. These data will be valuable to cell biologists who are interested in the nanoscale organization of yeasts and of eukaryotic cells in general. All the unpublished tilt series and a subset of corresponding cryotomograms have been deposited in the EMPIAR resource for the community to use freely. To improve tilt series discoverability, we have uploaded metadata and preliminary notes to publicly accessible Google Sheets, EMPIAR, and GigaDB. CONCLUSIONS Cellular cryo-ET data can be mined to obtain new cell-biological, structural, and 3D statistical insights in situ. These data contain structures not visible in traditional electron-microscopy data. Template matching and subtomogram averaging of known macromolecular complexes can reveal their 3D distributions and low-resolution structures. Furthermore, these data can serve as testbeds for high-throughput image-analysis pipelines, as training sets for feature-recognition software, for feasibility analysis when planning new structural-cell-biology projects, and as practice data for students.
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Affiliation(s)
- Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Chen Chen
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Shujun Cai
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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87
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Simeon R, Jiang M, Chamoun-Emanuelli AM, Yu H, Zhang Y, Meng R, Peng Z, Jakana J, Zhang J, Feng H, Chen Z. Selection and characterization of ultrahigh potency designed ankyrin repeat protein inhibitors of C. difficile toxin B. PLoS Biol 2019; 17:e3000311. [PMID: 31233493 PMCID: PMC6590788 DOI: 10.1371/journal.pbio.3000311] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 05/20/2019] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile infection (CDI) is a major nosocomial disease associated with significant morbidity and mortality. The pathology of CDI stems primarily from the 2 C. difficile-secreted exotoxins-toxin A (TcdA) and toxin B (TcdB)-that disrupt the tight junctions between epithelial cells leading to the loss of colonic epithelial barrier function. Here, we report the engineering of a series of monomeric and dimeric designed ankyrin repeat proteins (DARPins) for the neutralization of TcdB. The best dimeric DARPin, DLD-4, inhibited TcdB with a half maximal effective concentration (EC50) of 4 pM in vitro, representing an approximately 330-fold higher potency than the Food and Drug Administration (FDA)-approved anti-TcdB monoclonal antibody bezlotoxumab in the same assay. DLD-4 also protected mice from a toxin challenge in vivo. Cryo-electron microscopy (cryo-EM) studies revealed that the 2 constituent DARPins of DLD-4-1.4E and U3-bind the central and C-terminal regions of the delivery domain of TcdB. Competitive enzyme-linked immunosorbent assay (ELISA) studies showed that the DARPins 1.4E and U3 interfere with the interaction between TcdB and its receptors chondroitin sulfate proteoglycan 4 (CSPG4) and frizzled class receptor 2 (FZD2), respectively. Our cryo-EM studies revealed a new conformation of TcdB (both apo- and DARPin-bound at pH 7.4) in which the combined repetitive oligopeptides (CROPS) domain points away from the delivery domain. This conformation of the CROPS domain is in stark contrast to that seen in the negative-stain electron microscopy (EM) structure of TcdA and TcdB at the same pH, in which the CROPS domain bends toward and "kisses" the delivery domain. The ultrapotent anti-TcdB molecules from this study serve as candidate starting points for CDI drug development and provide new biological tools for studying the pathogenicity of C. difficile. The structural insights regarding both the "native" conformation of TcdB and the putative sites of TcdB interaction with the FZD2 receptor, in particular, should help accelerate the development of next-generation anti-C. difficile toxin therapeutics.
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Affiliation(s)
- Rudo Simeon
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, United States of America
| | - Mengqiu Jiang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Ana M. Chamoun-Emanuelli
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, United States of America
| | - Hua Yu
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, Maryland, United Sates of America
| | - Yongrong Zhang
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, Maryland, United Sates of America
| | - Ran Meng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Zeyu Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, United States of America
| | - Joanita Jakana
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Hanping Feng
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, Maryland, United Sates of America
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, United States of America
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88
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Abstract
We report a complete 3D structural model of typical epithelial primary cilia based on structural maps of full-length primary cilia obtained by serial section electron tomography. Our data demonstrate the architecture of primary cilia differs extensively from the commonly acknowledged 9+0 paradigm. The axoneme structure is relatively stable but gradually evolves from base to tip with a decreasing number of microtubule complexes (MtCs) and a reducing diameter. The axonemal MtCs are cross-linked by previously unrecognized fibrous protein networks. Such an architecture explains why primary cilia can elastically withstand liquid flow for mechanosensing. The nine axonemal MtCs in a cilium are found to differ significantly in length indicating intraflagellar transport processes in primary cilia may be more complicated than that reported for motile cilia. The 3D maps of microtubule doublet-singlet transitions generally display longitudinal gaps at the inner junction between the A- and B-tubules, which indicates the inner junction protein is a major player in doublet-singlet transitions. In addition, vesicles releasing from kidney primary cilia were observed in the structural maps, supporting that ciliary vesicles budding may serve as ectosomes for cell-cell communication.
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89
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Chen Q, Zeng W, She J, Bai XC, Jiang Y. Structural and functional characterization of an otopetrin family proton channel. eLife 2019; 8:46710. [PMID: 30973323 PMCID: PMC6483595 DOI: 10.7554/elife.46710] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 04/11/2019] [Indexed: 12/14/2022] Open
Abstract
The otopetrin (OTOP) proteins were recently characterized as proton channels. Here we present the cryo-EM structure of OTOP3 from Xenopus tropicalis (XtOTOP3) along with functional characterization of the channel. XtOTOP3 forms a homodimer with each subunit containing 12 transmembrane helices that can be divided into two structurally homologous halves; each half assembles as an α-helical barrel that could potentially serve as a proton conduction pore. Both pores open from the extracellular half before becoming occluded at a central constriction point consisting of three highly conserved residues - Gln232/585-Asp262/Asn623-Tyr322/666 (the constriction triads). Mutagenesis shows that the constriction triad from the second pore is less amenable to perturbation than that of the first pore, suggesting an unequal contribution between the two pores to proton transport. We also identified several key residues at the interface between the two pores that are functionally important, particularly Asp509, which confers intracellular pH-dependent desensitization to OTOP channels.
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Affiliation(s)
- Qingfeng Chen
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Weizhong Zeng
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ji She
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Youxing Jiang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
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90
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Rollins MF, Chowdhury S, Carter J, Golden SM, Miettinen HM, Santiago-Frangos A, Faith D, Lawrence CM, Lander GC, Wiedenheft B. Structure Reveals a Mechanism of CRISPR-RNA-Guided Nuclease Recruitment and Anti-CRISPR Viral Mimicry. Mol Cell 2019; 74:132-142.e5. [PMID: 30872121 PMCID: PMC6521718 DOI: 10.1016/j.molcel.2019.02.001] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/21/2018] [Accepted: 01/30/2019] [Indexed: 12/14/2022]
Abstract
Bacteria and archaea have evolved sophisticated adaptive immune systems that rely on CRISPR RNA (crRNA)-guided detection and nuclease-mediated elimination of invading nucleic acids. Here, we present the cryo-electron microscopy (cryo-EM) structure of the type I-F crRNA-guided surveillance complex (Csy complex) from Pseudomonas aeruginosa bound to a double-stranded DNA target. Comparison of this structure to previously determined structures of this complex reveals a ∼180-degree rotation of the C-terminal helical bundle on the "large" Cas8f subunit. We show that the double-stranded DNA (dsDNA)-induced conformational change in Cas8f exposes a Cas2/3 "nuclease recruitment helix" that is structurally homologous to a virally encoded anti-CRISPR protein (AcrIF3). Structural homology between Cas8f and AcrIF3 suggests that AcrIF3 is a mimic of the Cas8f nuclease recruitment helix.
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MESH Headings
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/immunology
- Bacterial Proteins/metabolism
- CRISPR-Associated Proteins/chemistry
- CRISPR-Associated Proteins/genetics
- CRISPR-Associated Proteins/immunology
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems
- Clustered Regularly Interspaced Short Palindromic Repeats
- Cryoelectron Microscopy
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Models, Molecular
- Molecular Mimicry
- Nucleic Acid Conformation
- Protein Conformation
- Pseudomonas aeruginosa/enzymology
- Pseudomonas aeruginosa/genetics
- Pseudomonas aeruginosa/immunology
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Guide, CRISPR-Cas Systems/chemistry
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Structure-Activity Relationship
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/immunology
- Viral Proteins/metabolism
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Affiliation(s)
- MaryClare F Rollins
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Saikat Chowdhury
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA
| | - Joshua Carter
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Sarah M Golden
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Heini M Miettinen
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | | | - Dominick Faith
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - C Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research Institute, La Jolla, CA, USA.
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.
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91
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McNulty R, Cardone G, Gilcrease EB, Baker TS, Casjens SR, Johnson JE. Cryo-EM Elucidation of the Structure of Bacteriophage P22 Virions after Genome Release. Biophys J 2019; 114:1295-1301. [PMID: 29590587 DOI: 10.1016/j.bpj.2018.01.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/24/2017] [Accepted: 01/17/2018] [Indexed: 11/19/2022] Open
Abstract
Genome ejection proteins are required to facilitate transport of bacteriophage P22 double-stranded DNA safely through membranes of Salmonella. The structures and locations of all proteins in the context of the mature virion are known, with the exception of three ejection proteins. Furthermore, the changes that occur to the proteins residing in the mature virion upon DNA release are not fully understood. We used cryogenic electron microscopy to obtain what is, to our knowledge, the first asymmetric reconstruction of mature bacteriophage P22 after double-stranded DNA has been extruded from the capsid-a state representative of one step during viral infection. Results of icosahedral and asymmetric reconstructions at estimated resolutions of 7.8 and 12.5 Å resolutions, respectively, are presented. The reconstruction shows tube-like protein density extending from the center of the tail assembly. The portal protein does not revert to the more contracted, procapsid state, but instead maintains an extended and splayed barrel structure. These structural details contribute to our understanding of the molecular mechanism of P22 phage infection and also set the foundation for future exploitation serving engineering purposes.
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Affiliation(s)
- Reginald McNulty
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California.
| | - Giovanni Cardone
- Department of Chemistry and BiochemistryUniversity of California, San Diego, La Jolla, California
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah
| | - Timothy S Baker
- Department of Chemistry and BiochemistryUniversity of California, San Diego, La Jolla, California; Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California.
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92
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Krystofiak ES, Heymann JB, Kachar B. Carbon replicas reveal double stranded structure of tight junctions in phase-contrast electron microscopy. Commun Biol 2019; 2:98. [PMID: 30886907 PMCID: PMC6414538 DOI: 10.1038/s42003-019-0319-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
Replica-based freeze-fracture and freeze-etching electron microscopy methods provide surface topography information, particularly suited to studying membrane protein complexes in their native context. The fidelity and resolution of metal replicas is limited by the inherent property of metal atoms to crystallize. To overcome the limitations of metal replicas, we combined amorphous carbon replicas with phase-contrast electron microscopy. Using this approach, tight junction intramembrane fibrils were shown to have a double stranded morphology.
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Affiliation(s)
- Evan S Krystofiak
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA.,Cell Imaging Shared Resource, Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37240, USA
| | - J Bernard Heymann
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bechara Kachar
- Laboratory of Cell Structure and Dynamics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, 20892, USA.
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93
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Bowler M, Kong D, Sun S, Nanjundappa R, Evans L, Farmer V, Holland A, Mahjoub MR, Sui H, Loncarek J. High-resolution characterization of centriole distal appendage morphology and dynamics by correlative STORM and electron microscopy. Nat Commun 2019; 10:993. [PMID: 30824690 PMCID: PMC6397210 DOI: 10.1038/s41467-018-08216-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 12/10/2018] [Indexed: 12/17/2022] Open
Abstract
Centrioles are vital cellular structures that form centrosomes and cilia. The formation and function of cilia depends on a set of centriole's distal appendages. In this study, we use correlative super resolution and electron microscopy to precisely determine where distal appendage proteins localize in relation to the centriole microtubules and appendage electron densities. Here we characterize a novel distal appendage protein ANKRD26 and detail, in high resolution, the initial steps of distal appendage assembly. We further show that distal appendages undergo a dramatic ultra-structural reorganization before mitosis, during which they temporarily lose outer components, while inner components maintain a nine-fold organization. Finally, using electron tomography we reveal that mammalian distal appendages associate with two centriole microtubule triplets via an elaborate filamentous base and that they appear as almost radial finger-like protrusions. Our findings challenge the traditional portrayal of mammalian distal appendage as a pinwheel-like structure that is maintained throughout mitosis.
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Affiliation(s)
- Mathew Bowler
- Laboratory of Protein Dynamics and Signaling, NIH/NCI/CCR, Frederick, Maryland, 21702, USA
- Optical Microscopy and Analysis Laboratory, NIH/NCI/CCR, Frederick, Maryland, 21702, USA
| | - Dong Kong
- Laboratory of Protein Dynamics and Signaling, NIH/NCI/CCR, Frederick, Maryland, 21702, USA
| | - Shufeng Sun
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
| | - Rashmi Nanjundappa
- Department of Medicine (Nephrology Division), Washington University, St Louis, 63110, MO, USA
| | - Lauren Evans
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, 21205, MD, USA
| | - Veronica Farmer
- Laboratory of Protein Dynamics and Signaling, NIH/NCI/CCR, Frederick, Maryland, 21702, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, 37235, TN, USA
| | - Andrew Holland
- Department of Molecular Biology & Genetics, Johns Hopkins University School of Medicine, Baltimore, 21205, MD, USA
| | - Moe R Mahjoub
- Department of Medicine (Nephrology Division), Washington University, St Louis, 63110, MO, USA
- Department of Cell Biology and Physiology, Washington University, St Louis, 12201, MO, USA
| | - Haixin Sui
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201, USA
- Department of Biomedical Sciences, School of Public Health, University of Albany, Albany, NY, 12201, USA
| | - Jadranka Loncarek
- Laboratory of Protein Dynamics and Signaling, NIH/NCI/CCR, Frederick, Maryland, 21702, USA.
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94
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El Omari K, Li S, Kotecha A, Walter TS, Bignon EA, Harlos K, Somerharju P, De Haas F, Clare DK, Molin M, Hurtado F, Li M, Grimes JM, Bamford DH, Tischler ND, Huiskonen JT, Stuart DI, Roine E. The structure of a prokaryotic viral envelope protein expands the landscape of membrane fusion proteins. Nat Commun 2019; 10:846. [PMID: 30783086 PMCID: PMC6381117 DOI: 10.1038/s41467-019-08728-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 01/22/2019] [Indexed: 11/09/2022] Open
Abstract
Lipid membrane fusion is an essential function in many biological processes. Detailed mechanisms of membrane fusion and the protein structures involved have been mainly studied in eukaryotic systems, whereas very little is known about membrane fusion in prokaryotes. Haloarchaeal pleomorphic viruses (HRPVs) have a membrane envelope decorated with spikes that are presumed to be responsible for host attachment and membrane fusion. Here we determine atomic structures of the ectodomains of the 57-kDa spike protein VP5 from two related HRPVs revealing a previously unreported V-shaped fold. By Volta phase plate cryo-electron tomography we show that VP5 is monomeric on the viral surface, and we establish the orientation of the molecules with respect to the viral membrane. We also show that the viral membrane fuses with the host cytoplasmic membrane in a process mediated by VP5. This sheds light on protein structures involved in prokaryotic membrane fusion.
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Affiliation(s)
- Kamel El Omari
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Sai Li
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Thomas S Walter
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Eduardo A Bignon
- Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Pentti Somerharju
- Department of Biochemistry and Developmental Biology, University of Helsinki, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Felix De Haas
- Thermo Fisher Scientific, Achtseweg Noorg 5, 5651 GG, Eindhoven, The Netherlands
| | - Daniel K Clare
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Mika Molin
- Helsinki Institute of Life Science HiLIFE, Institute of Biotechnology, University of Helsinki, Viikinkaari 5, 00014, Helsinki, Finland
| | - Felipe Hurtado
- Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile
| | - Mengqiu Li
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Dennis H Bamford
- Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
| | - Nicole D Tischler
- Fundación Ciencia & Vida, Laboratorio de Virología Molecular, Avenida Zañartu 1482, 7780272, Ñuñoa, Santiago, Chile.
| | - Juha T Huiskonen
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Helsinki Institute of Life Science HiLIFE and Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland.
| | - David I Stuart
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Elina Roine
- Molecular and Integrative Biosciences Research Program, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland.
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95
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Li S, Fernandez JJ, Marshall WF, Agard DA. Electron cryo-tomography provides insight into procentriole architecture and assembly mechanism. eLife 2019; 8:43434. [PMID: 30741631 PMCID: PMC6384029 DOI: 10.7554/elife.43434] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/10/2019] [Indexed: 01/03/2023] Open
Abstract
Centriole is an essential structure with multiple functions in cellular processes. Centriole biogenesis and homeostasis is tightly regulated. Using electron cryo-tomography (cryoET) we present the structure of procentrioles from Chlamydomonas reinhardtii. We identified a set of non-tubulin components attached to the triplet microtubule (MT), many are at the junctions of tubules likely to reinforce the triplet. We describe structure of the A-C linker that bridges neighboring triplets. The structure infers that POC1 is likely an integral component of A-C linker. Its conserved WD40 β-propeller domain provides attachment sites for other A-C linker components. The twist of A-C linker results in an iris diaphragm-like motion of the triplets in the longitudinal direction of procentriole. Finally, we identified two assembly intermediates at the growing ends of procentriole allowing us to propose a model for the procentriole assembly. Our results provide a comprehensive structural framework for understanding the molecular mechanisms underpinning procentriole biogenesis and assembly.
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Affiliation(s)
- Sam Li
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Wallace F Marshall
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - David A Agard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
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96
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Koehl A, Hu H, Feng D, Sun B, Zhang Y, Robertson MJ, Chu M, Kobilka TS, Laeremans T, Steyaert J, Tarrasch J, Dutta S, Fonseca R, Weis WI, Mathiesen JM, Skiniotis G, Kobilka BK. Structural insights into the activation of metabotropic glutamate receptors. Nature 2019; 566:79-84. [PMID: 30675062 PMCID: PMC6709600 DOI: 10.1038/s41586-019-0881-4] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
Metabotropic glutamate receptors are family C G-protein-coupled receptors. They form obligate dimers and possess extracellular ligand-binding Venus flytrap domains, which are linked by cysteine-rich domains to their 7-transmembrane domains. Spectroscopic studies show that signalling is a dynamic process, in which large-scale conformational changes underlie the transmission of signals from the extracellular Venus flytraps to the G protein-coupling domains-the 7-transmembrane domains-in the membrane. Here, using a combination of X-ray crystallography, cryo-electron microscopy and signalling studies, we present a structural framework for the activation mechanism of metabotropic glutamate receptor subtype 5. Our results show that agonist binding at the Venus flytraps leads to a compaction of the intersubunit dimer interface, thereby bringing the cysteine-rich domains into close proximity. Interactions between the cysteine-rich domains and the second extracellular loops of the receptor enable the rigid-body repositioning of the 7-transmembrane domains, which come into contact with each other to initiate signalling.
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Affiliation(s)
- Antoine Koehl
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongli Hu
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dan Feng
- ConfometRx, Santa Clara, CA, USA
| | | | - Yan Zhang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Robertson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tong Sun Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,ConfometRx, Santa Clara, CA, USA
| | - Toon Laeremans
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jeffrey Tarrasch
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Somnath Dutta
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Rasmus Fonseca
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - William I Weis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jesper M Mathiesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Georgios Skiniotis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. .,ConfometRx, Santa Clara, CA, USA.
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97
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Mitra AK. Visualization of biological macromolecules at near-atomic resolution: cryo-electron microscopy comes of age. Acta Crystallogr F Struct Biol Commun 2019; 75:3-11. [PMID: 30605120 PMCID: PMC6317457 DOI: 10.1107/s2053230x18015133] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/26/2018] [Indexed: 11/11/2022] Open
Abstract
Structural biology is going through a revolution as a result of transformational advances in the field of cryo-electron microscopy (cryo-EM) driven by the development of direct electron detectors and ultrastable electron microscopes. High-resolution cryo-EM images of isolated biomolecules (single particles) suspended in a thin layer of vitrified buffer are subjected to powerful image-processing algorithms, enabling near-atomic resolution structures to be determined in unprecedented numbers. Prior to these advances, electron crystallography of two-dimensional crystals and helical assemblies of proteins had established the feasibility of atomic resolution structure determination using cryo-EM. Atomic resolution single-particle analysis, without the need for crystals, now promises to resolve problems in structural biology that were intractable just a few years ago.
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MESH Headings
- Algorithms
- Bibliometrics
- Cryoelectron Microscopy/history
- Cryoelectron Microscopy/instrumentation
- Cryoelectron Microscopy/methods
- Crystallography, X-Ray/history
- Crystallography, X-Ray/instrumentation
- Crystallography, X-Ray/methods
- Equipment Design/history
- History, 20th Century
- History, 21st Century
- Humans
- Image Processing, Computer-Assisted/statistics & numerical data
- Imaging, Three-Dimensional/instrumentation
- Imaging, Three-Dimensional/methods
- Macromolecular Substances/chemistry
- Macromolecular Substances/ultrastructure
- Microscopy, Electron, Transmission/history
- Microscopy, Electron, Transmission/instrumentation
- Microscopy, Electron, Transmission/methods
- Specimen Handling/instrumentation
- Specimen Handling/methods
- Vitrification
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Affiliation(s)
- Alok K. Mitra
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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98
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Studying the Spatial Organization of ESCRTs in Cytokinetic Abscission Using the High-Resolution Imaging Techniques SIM and Cryo-SXT. Methods Mol Biol 2019; 1998:129-148. [PMID: 31250299 DOI: 10.1007/978-1-4939-9492-2_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The ESCRT machinery mediates scission of the intercellular bridge that connects two daughter cells at the end of cytokinesis. Structured illumination microscopy (SIM) and cryo-soft-X-ray tomography (cryo-SXT) have been used in recent years to study the topology of ESCRT-driven cytokinetic abscission. These studies revealed that the intercellular bridge is occupied by cortical rings and spiral-like filaments and that ESCRTs form ring-like structures in this region during abscission. In this chapter, we provide two protocols: a protocol for determining the spatial organization of specific ESCRT components at the intercellular bridge using SIM and a protocol for resolving the ultrastructural organization of cortical filaments at the intercellular bridge using cryo-SXT.
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99
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Wong W, Huang R, Menant S, Hong C, Sandow JJ, Birkinshaw RW, Healer J, Hodder AN, Kanjee U, Tonkin CJ, Heckmann D, Soroka V, Søgaard TMM, Jørgensen T, Duraisingh MT, Czabotar PE, de Jongh WA, Tham WH, Webb AI, Yu Z, Cowman AF. Structure of Plasmodium falciparum Rh5-CyRPA-Ripr invasion complex. Nature 2018; 565:118-121. [PMID: 30542156 DOI: 10.1038/s41586-018-0779-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/25/2018] [Indexed: 01/24/2023]
Abstract
Plasmodium falciparum causes the severe form of malaria that has high levels of mortality in humans. Blood-stage merozoites of P. falciparum invade erythrocytes, and this requires interactions between multiple ligands from the parasite and receptors in hosts. These interactions include the binding of the Rh5-CyRPA-Ripr complex with the erythrocyte receptor basigin1,2, which is an essential step for entry into human erythrocytes. Here we show that the Rh5-CyRPA-Ripr complex binds the erythrocyte cell line JK-1 significantly better than does Rh5 alone, and that this binding occurs through the insertion of Rh5 and Ripr into host membranes as a complex with high molecular weight. We report a cryo-electron microscopy structure of the Rh5-CyRPA-Ripr complex at subnanometre resolution, which reveals the organization of this essential invasion complex and the mode of interactions between members of the complex, and shows that CyRPA is a critical mediator of complex assembly. Our structure identifies blades 4-6 of the β-propeller of CyRPA as contact sites for Rh5 and Ripr. The limited contacts between Rh5-CyRPA and CyRPA-Ripr are consistent with the dissociation of Rh5 and Ripr from CyRPA for membrane insertion. A comparision of the crystal structure of Rh5-basigin with the cryo-electron microscopy structure of Rh5-CyRPA-Ripr suggests that Rh5 and Ripr are positioned parallel to the erythrocyte membrane before membrane insertion. This provides information on the function of this complex, and thereby provides insights into invasion by P. falciparum.
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Affiliation(s)
- Wilson Wong
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Rick Huang
- CryoEM Shared Resources, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Sebastien Menant
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Chuan Hong
- CryoEM Shared Resources, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jarrod J Sandow
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Richard W Birkinshaw
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Julie Healer
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Anthony N Hodder
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Usheer Kanjee
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Christopher J Tonkin
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Denise Heckmann
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | | | | | | | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Peter E Czabotar
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | | | - Wai-Hong Tham
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew I Webb
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Zhiheng Yu
- CryoEM Shared Resources, Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Alan F Cowman
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia.
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100
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Myers JB, Haddad BG, O'Neill SE, Chorev DS, Yoshioka CC, Robinson CV, Zuckerman DM, Reichow SL. Structure of native lens connexin 46/50 intercellular channels by cryo-EM. Nature 2018; 564:372-377. [PMID: 30542154 PMCID: PMC6309215 DOI: 10.1038/s41586-018-0786-7] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/29/2018] [Indexed: 11/19/2022]
Abstract
Gap junctions establish direct pathways for cell-to-cell communication through the assembly of twelve connexin subunits that form intercellular channels connecting neighbouring cells. Co-assembly of different connexin isoforms produces channels with unique properties and enables communication across cell types. Here we used single-particle cryo-electron microscopy to investigate the structural basis of connexin co-assembly in native lens gap junction channels composed of connexin 46 and connexin 50 (Cx46/50). We provide the first comparative analysis to connexin 26 (Cx26), which-together with computational studies-elucidates key energetic features governing gap junction permselectivity. Cx46/50 adopts an open-state conformation that is distinct from the Cx26 crystal structure, yet it appears to be stabilized by a conserved set of hydrophobic anchoring residues. 'Hot spots' of genetic mutations linked to hereditary cataract formation map to the core structural-functional elements identified in Cx46/50, suggesting explanations for many of the disease-causing effects.
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Affiliation(s)
- Janette B Myers
- Department of Chemistry, Portland State University, Portland, OR, USA
| | - Bassam G Haddad
- Department of Chemistry, Portland State University, Portland, OR, USA
| | - Susan E O'Neill
- Department of Chemistry, Portland State University, Portland, OR, USA
| | - Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Craig C Yoshioka
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Steve L Reichow
- Department of Chemistry, Portland State University, Portland, OR, USA.
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