51
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TORC1 organized in inhibited domains (TOROIDs) regulate TORC1 activity. Nature 2017; 550:265-269. [PMID: 28976958 PMCID: PMC5640987 DOI: 10.1038/nature24021] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 08/21/2017] [Indexed: 12/17/2022]
Abstract
The Target of Rapamycin (TOR) is a eukaryotic serine/threonine protein kinase that functions in two distinct complexes, TORC1 and TORC2, to regulate growth and metabolism1,2. GTPases, responding to signals generated by abiotic stressors, nutrients, and, in metazoans, growth factors, play an important3, but poorly understood role in TORC1 regulation. Here, we report that, in budding yeast, glucose withdrawal, which leads to an acute loss of TORC1 kinase activity4, triggers a similarly rapid Rag GTPase-dependent redistribution of TORC1 from being semi-uniform around the vacuolar membrane to a single, vacuole-associated cylindrical structure visible by super-resolution optical microscopy. 3D reconstructions of cryo-electron micrograph images of these purified cylinders demonstrate that TORC1 oligomerizes into a higher-level hollow helical assembly which we name a TOROID (TORC1 Organised in Inhibited Domain). Fitting of the recently described mammalian TORC1 structure into our helical map revealed that oligomerisation leads to steric occlusion of the active site. Guided by the implications from our reconstruction, we present a TOR1 allele that prevents both TOROID formation and TORC1 inactivation in response to glucose withdrawal demonstrating that oligomerisation is necessary for TORC1 inactivation. Our results reveal a novel mechanism by which Rag-GTPases regulate TORC1 activity and suggest that the reversible assembly/disassembly of higher-level structure may be a new paradigm for the regulation of protein kinases.
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52
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Cryo-EM structure of the extended type VI secretion system sheath–tube complex. Nat Microbiol 2017; 2:1507-1512. [DOI: 10.1038/s41564-017-0020-7] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 08/02/2017] [Indexed: 11/08/2022]
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53
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Zamora M, Méndez-López E, Agirrezabala X, Cuesta R, Lavín JL, Sánchez-Pina MA, Aranda MA, Valle M. Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses. SCIENCE ADVANCES 2017; 3:eaao2182. [PMID: 28948231 PMCID: PMC5606705 DOI: 10.1126/sciadv.aao2182] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 08/18/2017] [Indexed: 05/16/2023]
Abstract
Potyviruses constitute the second largest genus of plant viruses and cause important economic losses in a large variety of crops; however, the atomic structure of their particles remains unknown. Infective potyvirus virions are long flexuous filaments where coat protein (CP) subunits assemble in helical mode bound to a monopartite positive-sense single-stranded RNA [(+)ssRNA] genome. We present the cryo-electron microscopy (cryoEM) structure of the potyvirus watermelon mosaic virus at a resolution of 4.0 Å. The atomic model shows a conserved fold for the CPs of flexible filamentous plant viruses, including a universally conserved RNA binding pocket, which is a potential target for antiviral compounds. This conserved fold of the CP is widely distributed in eukaryotic viruses and is also shared by nucleoproteins of enveloped viruses with segmented (-)ssRNA (negative-sense ssRNA) genomes, including influenza viruses.
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Affiliation(s)
- Miguel Zamora
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - Eduardo Méndez-López
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Espinardo, 30100 Murcia, Spain
| | - Xabier Agirrezabala
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - Rebeca Cuesta
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - José L. Lavín
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
| | - M. Amelia Sánchez-Pina
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Espinardo, 30100 Murcia, Spain
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Espinardo, 30100 Murcia, Spain
| | - Mikel Valle
- Molecular Recognition and Host-Pathogen Interactions, Center for Cooperative Research in Biosciences, CIC bioGUNE, 48160 Derio, Spain
- Corresponding author.
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54
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Alvarez FJD, He S, Perilla JR, Jang S, Schulten K, Engelman AN, Scheres SHW, Zhang P. CryoEM structure of MxB reveals a novel oligomerization interface critical for HIV restriction. SCIENCE ADVANCES 2017; 3:e1701264. [PMID: 28929138 PMCID: PMC5600524 DOI: 10.1126/sciadv.1701264] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/17/2017] [Indexed: 06/01/2023]
Abstract
Human dynamin-like, interferon-induced myxovirus resistance 2 (Mx2 or MxB) is a potent HIV-1 inhibitor. Antiviral activity requires both the amino-terminal region of MxB and protein oligomerization, each of which has eluded structural determination due to difficulties in protein preparation. We report that maltose binding protein-fused, full-length wild-type MxB purifies as oligomers and further self-assembles into helical arrays in physiological salt. Guanosine triphosphate (GTP), but not guanosine diphosphate, binding results in array disassembly, whereas subsequent GTP hydrolysis allows its reformation. Using cryo-electron microscopy (cryoEM), we determined the MxB assembly structure at 4.6 Å resolution, representing the first near-atomic resolution structure in the mammalian dynamin superfamily. The structure revealed previously described and novel MxB assembly interfaces. Mutational analyses demonstrated a critical role for one of the novel interfaces in HIV-1 restriction.
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Affiliation(s)
- Frances J. D. Alvarez
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Shaoda He
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Juan R. Perilla
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sooin Jang
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Klaus Schulten
- Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alan N. Engelman
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Sjors H. W. Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Headington, Oxford OX3 7BN, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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55
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Donchenko EK, Pechnikova EV, Mishyna MY, Manukhova TI, Sokolova OS, Nikitin NA, Atabekov JG, Karpova OV. Structure and properties of virions and virus-like particles derived from the coat protein of Alternanthera mosaic virus. PLoS One 2017; 12:e0183824. [PMID: 28837650 PMCID: PMC5570366 DOI: 10.1371/journal.pone.0183824] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/11/2017] [Indexed: 01/01/2023] Open
Abstract
Plant viruses and their virus-like particles (VLPs) have a lot of advantages for biotechnological applications including complete safety for humans. Alternanthera mosaic virus (AltMV) is a potentially promising object for design of novel materials. The 3D structures of AltMV virions and its VLPs were obtained by single particle EM at ~13Å resolution. The comparison of the reconstructions and a trypsin treatment revealed that AltMV CPs possesses a different fold in the presence (virions) and absence of viral RNA (VLPs). For the first time, the structure of morphologically similar virions and virus-like particles based on the coat protein of a helical filamentous plant virus is shown to be different. Despite this, both AltMV virions and VLPs are stable in a wide range of conditions. To provide a large amount of AltMV for biotechnology usage the isolation procedure was modified.
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Affiliation(s)
| | - Evgeniya V. Pechnikova
- Laboratory of Electron Microscopy, V.A. Shoubnikov Institute of Crystallography of Russian Academy of Sciences, Moscow, Russia
- Nano-, Bio-, Information, Cognitive, Socio-Humanistic (NBICS) Science and Technology Center, National Research Centre "Kurchatov Institute", Moscow, Russia
| | | | | | - Olga S. Sokolova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Olga V. Karpova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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56
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Raasakka A, Ruskamo S, Kowal J, Barker R, Baumann A, Martel A, Tuusa J, Myllykoski M, Bürck J, Ulrich AS, Stahlberg H, Kursula P. Membrane Association Landscape of Myelin Basic Protein Portrays Formation of the Myelin Major Dense Line. Sci Rep 2017; 7:4974. [PMID: 28694532 PMCID: PMC5504075 DOI: 10.1038/s41598-017-05364-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/26/2017] [Indexed: 01/06/2023] Open
Abstract
Compact myelin comprises most of the dry weight of myelin, and its insulative nature is the basis for saltatory conduction of nerve impulses. The major dense line (MDL) is a 3-nm compartment between two cytoplasmic leaflets of stacked myelin membranes, mostly occupied by a myelin basic protein (MBP) phase. MBP is an abundant myelin protein involved in demyelinating diseases, such as multiple sclerosis. The association of MBP with lipid membranes has been studied for decades, but the MBP-driven formation of the MDL remains elusive at the biomolecular level. We employed complementary biophysical methods, including atomic force microscopy, cryo-electron microscopy, and neutron scattering, to investigate the formation of membrane stacks all the way from MBP binding onto a single membrane leaflet to the organisation of a stable MDL. Our results support the formation of an amorphous protein phase of MBP between two membrane bilayers and provide a molecular model for MDL formation during myelination, which is of importance when understanding myelin assembly and demyelinating conditions.
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Affiliation(s)
- Arne Raasakka
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Salla Ruskamo
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Julia Kowal
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Robert Barker
- School of Physical Sciences, University of Kent, Canterbury, Kent, United Kingdom
- Institut Laue-Langevin (ILL), Grenoble, France
| | - Anne Baumann
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Division of Psychiatry, Haukeland University Hospital, Bergen, Norway
| | - Anne Martel
- Institut Laue-Langevin (ILL), Grenoble, France
| | - Jussi Tuusa
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Matti Myllykoski
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway.
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
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57
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Muschiol S, Erlendsson S, Aschtgen MS, Oliveira V, Schmieder P, de Lichtenberg C, Teilum K, Boesen T, Akbey U, Henriques-Normark B. Structure of the competence pilus major pilin ComGC in Streptococcus pneumoniae. J Biol Chem 2017; 292:14134-14146. [PMID: 28659339 PMCID: PMC5572924 DOI: 10.1074/jbc.m117.787671] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/14/2017] [Indexed: 01/23/2023] Open
Abstract
Type IV pili are important virulence factors on the surface of many pathogenic bacteria and have been implicated in a wide range of diverse functions, including attachment, twitching motility, biofilm formation, and horizontal gene transfer. The respiratory pathogen Streptococcus pneumoniae deploys type IV pili to take up DNA during transformation. These “competence pili” are composed of the major pilin protein ComGC and exclusively assembled during bacterial competence, but their biogenesis remains unclear. Here, we report the high resolution NMR structure of N-terminal truncated ComGC revealing a highly flexible and structurally divergent type IV pilin. It consists of only three α-helical segments forming a well-defined electronegative cavity and confined electronegative and hydrophobic patches. The structure is particularly flexible between the first and second α-helix with the first helical part exhibiting slightly slower dynamics than the rest of the pilin, suggesting that the first helix is involved in forming the pilus structure core and that parts of helices two and three are primarily surface-exposed. Taken together, our results provide the first structure of a type IV pilin protein involved in the formation of competence-induced pili in Gram-positive bacteria and corroborate the remarkable structural diversity among type IV pilin proteins.
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Affiliation(s)
- Sandra Muschiol
- From the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden,; Department of Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden,.
| | - Simon Erlendsson
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Center for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Marie-Stephanie Aschtgen
- From the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden,; Department of Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Vitor Oliveira
- From the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden,; Department of Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Peter Schmieder
- Leibniz-Institut für Molekulare Pharmakologie FMP, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Casper de Lichtenberg
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Center for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Center for Protein Science, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
| | - Thomas Boesen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Umit Akbey
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark,; Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Høegh-Guldbergs Gade 6B, 8000 Aarhus C, Denmark
| | - Birgitta Henriques-Normark
- From the Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden,; Department of Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden,; Singapore Centre on Environmental Life Sciences Engineering (SCELSE) and Lee Kong Chian School of Medicine (LKC), Nanyang Technological University, Singapore 639798, Singapore.
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58
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In vitro assembly of the Rous Sarcoma Virus capsid protein into hexamer tubes at physiological temperature. Sci Rep 2017; 7:2913. [PMID: 28588198 PMCID: PMC5460288 DOI: 10.1038/s41598-017-02060-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 04/06/2017] [Indexed: 12/21/2022] Open
Abstract
During a proteolytically-driven maturation process, the orthoretroviral capsid protein (CA) assembles to form the convex shell that surrounds the viral genome. In some orthoretroviruses, including Rous Sarcoma Virus (RSV), CA carries a short and hydrophobic spacer peptide (SP) at its C-terminus early in the maturation process, which is progressively removed as maturation proceeds. In this work, we show that RSV CA assembles in vitro at near-physiological temperatures, forming hexamer tubes that effectively model the mature capsid surface. Tube assembly is strongly influenced by electrostatic effects, and is a nucleated process that remains thermodynamically favored at lower temperatures, but is effectively arrested by the large Gibbs energy barrier associated with nucleation. RSV CA tubes are multi-layered, being formed by nested and concentric tubes of capsid hexamers. However the spacer peptide acts as a layering determinant during tube assembly. If only a minor fraction of CA-SP is present, multi-layered tube formation is blocked, and single-layered tubes predominate. This likely prevents formation of biologically aberrant multi-layered capsids in the virion. The generation of single-layered hexamer tubes facilitated 3D helical image reconstruction from cryo-electron microscopy data, revealing the basic tube architecture.
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59
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Biyani N, Righetto RD, McLeod R, Caujolle-Bert D, Castano-Diez D, Goldie KN, Stahlberg H. Focus: The interface between data collection and data processing in cryo-EM. J Struct Biol 2017; 198:124-133. [PMID: 28344036 DOI: 10.1016/j.jsb.2017.03.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/17/2017] [Accepted: 03/20/2017] [Indexed: 12/15/2022]
Abstract
We present a new software package called Focus that interfaces cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner while new data is being acquired at the microscope. It provides the functionality required to remotely monitor the progress of data collection and data processing, which is essential now that automation in cryo-EM allows a steady flow of images of single particles, two-dimensional crystals, or electron tomography data to be recorded in overnight sessions. The rapid detection of any errors that may occur greatly increases the productivity of recording sessions at the electron microscope.
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Affiliation(s)
- Nikhil Biyani
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Ricardo D Righetto
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Robert McLeod
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | | | | | - Kenneth N Goldie
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Basel, Switzerland.
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60
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Mishyna M, Volokh O, Danilova Y, Gerasimova N, Pechnikova E, Sokolova OS. Effects of radiation damage in studies of protein-DNA complexes by cryo-EM. Micron 2017; 96:57-64. [PMID: 28262565 DOI: 10.1016/j.micron.2017.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/18/2017] [Accepted: 02/18/2017] [Indexed: 11/26/2022]
Abstract
Nucleic acids are responsible for the storage, transfer and realization of genetic information in the cell, which provides correct development and functioning of organisms. DNA interaction with ligands ensures the safety of this information. Over the past 10 years, advances in electron microscopy and image processing allowed to obtain the structures of key DNA-protein complexes with resolution below 4Å. However, radiation damage is a limiting factor to the potentially attainable resolution in cryo-EM. The prospect and limitations of studying protein-DNA complex interactions using cryo-electron microscopy are discussed here. We reviewed the ways to minimize radiation damage in biological specimens and the possibilities of using radiation damage (so-called 'bubblegrams') to obtain additional structural information.
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Affiliation(s)
- M Mishyna
- Lomonosov Moscow State University, 119234, Moscow, Russia.
| | - O Volokh
- Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Ya Danilova
- Lomonosov Moscow State University, 119234, Moscow, Russia
| | - N Gerasimova
- Lomonosov Moscow State University, 119234, Moscow, Russia
| | - E Pechnikova
- Thermo Fisher Scientific, Materials & Structural Analysis, 5651 GG Eindhoven, Netherlands
| | - O S Sokolova
- Lomonosov Moscow State University, 119234, Moscow, Russia.
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61
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He S, Scheres SHW. Helical reconstruction in RELION. J Struct Biol 2017; 198:163-176. [PMID: 28193500 PMCID: PMC5479445 DOI: 10.1016/j.jsb.2017.02.003] [Citation(s) in RCA: 321] [Impact Index Per Article: 45.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/24/2017] [Accepted: 02/09/2017] [Indexed: 01/15/2023]
Abstract
We describe a new implementation for the reconstruction of helical assemblies in the empirical Bayesian framework of RELION. Our approach calculates optimal linear filters for the 3D reconstruction by embedding helical symmetry operators in Fourier-space, and deals with deviations from perfect helical symmetry through Gaussian-shaped priors on the orientations of individual segments. By incorporating our approach into the standard pipeline for single-particle analysis in RELION, our implementation aims to be easily accessible for non-experienced users. Although our implementation does not solve the problem that grossly incorrect structures can be obtained when the wrong helical symmetry is imposed, we show for four different test cases that it is capable of reconstructing structures to near-atomic resolution.
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Affiliation(s)
- Shaoda He
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH Cambridge, UK
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, CB2 0QH Cambridge, UK.
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62
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Merino F, Raunser S. Kryo-Elektronenmikroskopie als Methode für die strukturbasierte Wirkstoffentwicklung. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201608432] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Felipe Merino
- Strukturelle Biochemie; Max-Planck-Institut für Molekulare Physiologie; 44227 Dortmund Deutschland
| | - Stefan Raunser
- Strukturelle Biochemie; Max-Planck-Institut für Molekulare Physiologie; 44227 Dortmund Deutschland
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63
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Merino F, Raunser S. Electron Cryo-microscopy as a Tool for Structure-Based Drug Development. Angew Chem Int Ed Engl 2017; 56:2846-2860. [PMID: 27860084 DOI: 10.1002/anie.201608432] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Indexed: 12/15/2022]
Abstract
For decades, X-ray crystallography and NMR have been the most important techniques for studying the atomic structure of macromolecules. However, as a result of size, instability, low yield, and other factors, many macromolecules are difficult to crystallize or unsuitable for NMR studies. Electron cryo-microscopy (cryo-EM) does not depend on crystals and has therefore been the method of choice for many macromolecular complexes that cannot be crystallized, but atomic resolution has mostly been beyond its reach. A new generation of detectors that are capable of sensing directly the incident electrons has recently revolutionized the field, with structures of macromolecules now routinely being solved to near-atomic resolution. In this review, we summarize some of the most recent examples of high-resolution cryo-EM structures. We put particular emphasis on proteins with pharmacological relevance that have traditionally been inaccessible to crystallography. Furthermore, we discuss examples where interactions with small molecules have been fully characterized at atomic resolution. Finally, we stress the current limits of cryo-EM, and methodological issues related to its usage as a tool for drug development.
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Affiliation(s)
- Felipe Merino
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
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64
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Complete structure of the bacterial flagellar hook reveals extensive set of stabilizing interactions. Nat Commun 2016; 7:13425. [PMID: 27811912 PMCID: PMC5097172 DOI: 10.1038/ncomms13425] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/03/2016] [Indexed: 11/15/2022] Open
Abstract
The bacterial flagellar hook is a tubular helical structure made by the polymerization of multiple copies of a protein, FlgE. Here we report the structure of the hook from Campylobacter jejuni by cryo-electron microscopy at a resolution of 3.5 Å. On the basis of this structure, we show that the hook is stabilized by intricate inter-molecular interactions between FlgE molecules. Extra domains in FlgE, found only in Campylobacter and in related bacteria, bring more stability and robustness to the hook. Functional experiments suggest that Campylobacter requires an unusually strong hook to swim without its flagella being torn off. This structure reveals details of the quaternary organization of the hook that consists of 11 protofilaments. Previous study of the flagellar filament of Campylobacter by electron microscopy showed its quaternary structure made of seven protofilaments. Therefore, this study puts in evidence the difference between the quaternary structures of a bacterial filament and its hook. The bacterial flagellar hook is made up of many copies of the protein FlgE. Here, the authors report the full structure of the hook from Campylobacter jejuni and show that its overall structure is different from that of the previously published filament.
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Coudray N, Lasala R, Zhang Z, Clark KM, Dumont ME, Stokes DL. Deducing the symmetry of helical assemblies: Applications to membrane proteins. J Struct Biol 2016; 195:167-178. [PMID: 27255388 DOI: 10.1016/j.jsb.2016.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 11/30/2022]
Abstract
Helical reconstruction represents a convenient and powerful approach for structure determination of macromolecules that assemble into helical arrays. In the case of membrane proteins, formation of tubular crystals with helical symmetry represents an attractive alternative, especially when their small size precludes the use of single-particle analysis. An essential first step for helical reconstruction is to characterize the helical symmetry. This process is often daunting, due to the complexity of helical diffraction and to the low signal-to-noise ratio in images of individual assemblies. Furthermore, the large diameters of the tubular crystals produced by membrane proteins exacerbates the innate ambiguities that, if not resolved, will produce incorrect structures. In this report, we describe a set of tools that can be used to eliminate ambiguities and to validate the choice of symmetry. The first approach increases the signal-to-noise ratio along layer lines by incoherently summing data from multiple helical assemblies, thus producing several candidate indexing schemes. The second approach compares the layer lines from images with those from synthetic models built with the various candidate schemes. The third approach uses unit cell dimensions measured from collapsed tubes to distinguish between these candidate schemes. These approaches are illustrated with tubular crystals from a boron transporter from yeast, Bor1p, and a β-barrel channel from the outer membrane of E. coli, OmpF.
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Affiliation(s)
- Nicolas Coudray
- Skirball Institute for Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, United States
| | - Ralph Lasala
- Skirball Institute for Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, United States
| | - Zhening Zhang
- Skirball Institute for Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, United States
| | - Kathy M Clark
- Department of Pediatrics and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14652, United States
| | - Mark E Dumont
- Department of Pediatrics and Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY 14652, United States
| | - David L Stokes
- Skirball Institute for Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, United States
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66
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Structures of Human Peroxiredoxin 3 Suggest Self-Chaperoning Assembly that Maintains Catalytic State. Structure 2016; 24:1120-9. [PMID: 27238969 DOI: 10.1016/j.str.2016.04.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/14/2016] [Accepted: 04/09/2016] [Indexed: 01/05/2023]
Abstract
Peroxiredoxins are antioxidant proteins primarily responsible for detoxification of hydroperoxides in cells. On exposure to various cellular stresses, peroxiredoxins can acquire chaperone activity, manifested as quaternary reorganization into a high molecular weight (HMW) form. Acidification, for example, causes dodecameric rings of human peroxiredoxin 3 (HsPrx3) to stack into long helical filaments. In this work, a 4.1-Å resolution structure of low-pH-instigated helical filaments was elucidated, showing a locally unfolded active site and partially folded C terminus. A 2.8-Å crystal structure of HsPrx3 was determined at pH 8.5 under reducing conditions, wherein dodecameric rings are arranged as a short stack, with symmetry similar to low-pH filaments. In contrast to previous observations, the crystal structure displays both a fully folded active site and ordered C terminus, suggesting that the HsPrx3 HMW form maintains catalytic activity. We propose a new role for the HMW form as a self-chaperoning assembly maintaining HsPrx3 function under stress.
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MpUL-multi: Software for Calculation of Amyloid Fibril Mass per Unit Length from TB-TEM Images. Sci Rep 2016; 6:21078. [PMID: 26867957 PMCID: PMC4751569 DOI: 10.1038/srep21078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/18/2016] [Indexed: 01/05/2023] Open
Abstract
Structure determination for amyloid fibrils presents many challenges due to the high variability exhibited by fibrils and heterogeneous morphologies present, even in single samples. Mass per unit length (MPL) estimates can be used to differentiate amyloid fibril morphologies and provide orthogonal evidence for helical symmetry parameters determined by other methods. In addition, MPL data can provide insight on the arrangement of subunits in a fibril, especially for more complex fibrils assembled with multiple parallel copies of the asymmetric unit or multiple twisted protofilaments. By detecting only scattered electrons, which serve as a relative measure of total scattering, and therefore protein mass, dark field imaging gives an approximation of the total mass of protein present in any given length of fibril. When compared with a standard of known MPL, such as Tobacco Mosaic Virus (TMV), MPL of the fibrils in question can be determined. The program suite MpUL-multi was written for rapid semi-automated processing of TB-TEM dark field data acquired using this method. A graphical user interface allows for simple designation of fibrils and standards. A second program averages intensities from multiple TMV molecules for accurate standard determination, makes multiple measurements along a given fibril, and calculates the MPL.
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68
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Fromm S, Sachse C. Cryo-EM Structure Determination Using Segmented Helical Image Reconstruction. Methods Enzymol 2016; 579:307-28. [DOI: 10.1016/bs.mie.2016.05.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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69
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Agirrezabala X, Méndez-López E, Lasso G, Sánchez-Pina MA, Aranda M, Valle M. The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses. eLife 2015; 4:e11795. [PMID: 26673077 PMCID: PMC4739775 DOI: 10.7554/elife.11795] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 12/15/2015] [Indexed: 11/23/2022] Open
Abstract
Flexible filamentous viruses include economically important plant pathogens. Their viral particles contain several hundred copies of a helically arrayed coat protein (CP) protecting a (+)ssRNA. We describe here a structure at 3.9 Å resolution, from electron cryomicroscopy, of Pepino mosaic virus (PepMV), a representative of the genus Potexvirus (family Alphaflexiviridae). Our results allow modeling of the CP and its interactions with viral RNA. The overall fold of PepMV CP resembles that of nucleoproteins (NPs) from the genus Phlebovirus (family Bunyaviridae), a group of enveloped (-)ssRNA viruses. The main difference between potexvirus CP and phlebovirus NP is in their C-terminal extensions, which appear to determine the characteristics of the distinct multimeric assemblies – a flexuous, helical rod or a loose ribonucleoprotein. The homology suggests gene transfer between eukaryotic (+) and (-)ssRNA viruses. DOI:http://dx.doi.org/10.7554/eLife.11795.001 A group of “flexible filamentous” viruses can cause serious diseases in a wide variety of crops and other plants. Each virus particle contains a single molecule called ribonucleic acid (RNA), which is protected by hundreds of copies of a coat protein. The RNA and coat proteins are arranged in a helical fashion to make a flexible rod-shaped particle. The flexibility of these viruses makes it difficult to carry out in-depth studies of their three-dimensional structures. As a result, we do not know how the RNA and coat proteins interact to form the structure of each virus particle. Agirrezabala et al. used a technique called cryo-electron microscopy (or cryoEM for short) to generate a highly detailed three-dimensional model of a flexible filamentous virus called Pepino Mosaic Virus. Agirezabala et al.’s findings reveal how the virus particles assemble, and the interactions between the coat protein and the ssRNA. Unexpectedly, the structure of the coat protein from Pepino Mosiac Virus is very similar to the structure of “nucleoproteins” from a group of viruses called the Phleboviruses, which infect animals. This similarity is striking and suggests that the gene that encodes these proteins has been transferred between the two groups of viruses during evolution. A future challenge is to find out whether this similarity extends to other groups of viruses. DOI:http://dx.doi.org/10.7554/eLife.11795.002
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Affiliation(s)
- Xabier Agirrezabala
- Structural Biology Unit, Center for Cooperative Research in Biosciences, Derio, Spain
| | - Eduardo Méndez-López
- Centro de Edafología y Biología Aplicada del Segura, Murcia, Spain.,Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | - Gorka Lasso
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, United States
| | - M Amelia Sánchez-Pina
- Centro de Edafología y Biología Aplicada del Segura, Murcia, Spain.,Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | - Miguel Aranda
- Centro de Edafología y Biología Aplicada del Segura, Murcia, Spain.,Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | - Mikel Valle
- Structural Biology Unit, Center for Cooperative Research in Biosciences, Derio, Spain
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70
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Bharat TA, Murshudov GN, Sachse C, Löwe J. Structures of actin-like ParM filaments show architecture of plasmid-segregating spindles. Nature 2015; 523:106-10. [PMID: 25915019 PMCID: PMC4493928 DOI: 10.1038/nature14356] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/02/2015] [Indexed: 12/03/2022]
Abstract
Active segregation of Escherichia coli low-copy-number plasmid R1 involves formation of a bipolar spindle made of left-handed double-helical actin-like ParM filaments. ParR links the filaments with centromeric parC plasmid DNA, while facilitating the addition of subunits to ParM filaments. Growing ParMRC spindles push sister plasmids to the cell poles. Here, using modern electron cryomicroscopy methods, we investigate the structures and arrangements of ParM filaments in vitro and in cells, revealing at near-atomic resolution how subunits and filaments come together to produce the simplest known mitotic machinery. To understand the mechanism of dynamic instability, we determine structures of ParM filaments in different nucleotide states. The structure of filaments bound to the ATP analogue AMPPNP is determined at 4.3 Å resolution and refined. The ParM filament structure shows strong longitudinal interfaces and weaker lateral interactions. Also using electron cryomicroscopy, we reconstruct ParM doublets forming antiparallel spindles. Finally, with whole-cell electron cryotomography, we show that doublets are abundant in bacterial cells containing low-copy-number plasmids with the ParMRC locus, leading to an asynchronous model of R1 plasmid segregation.
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Affiliation(s)
- Tanmay A.M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Garib N. Murshudov
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Carsten Sachse
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstr. 1, Heidelberg 69117, Germany
| | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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71
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Cryo-Electron Microscopy Structure of Human Peroxiredoxin-3 Filament Reveals the Assembly of a Putative Chaperone. Structure 2015; 23:912-920. [DOI: 10.1016/j.str.2015.03.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 03/21/2015] [Accepted: 03/23/2015] [Indexed: 01/07/2023]
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72
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Kudryashev M, Wang RYR, Brackmann M, Scherer S, Maier T, Baker D, DiMaio F, Stahlberg H, Egelman EH, Basler M. Structure of the type VI secretion system contractile sheath. Cell 2015; 160:952-962. [PMID: 25723169 DOI: 10.1016/j.cell.2015.01.037] [Citation(s) in RCA: 178] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/17/2014] [Accepted: 01/20/2015] [Indexed: 12/15/2022]
Abstract
Bacteria use rapid contraction of a long sheath of the type VI secretion system (T6SS) to deliver effectors into a target cell. Here, we present an atomic-resolution structure of a native contracted Vibrio cholerae sheath determined by cryo-electron microscopy. The sheath subunits, composed of tightly interacting proteins VipA and VipB, assemble into a six-start helix. The helix is stabilized by a core domain assembled from four β strands donated by one VipA and two VipB molecules. The fold of inner and middle layers is conserved between T6SS and phage sheaths. However, the structure of the outer layer is distinct and suggests a mechanism of interaction of the bacterial sheath with an accessory ATPase, ClpV, that facilitates multiple rounds of effector delivery. Our results provide a mechanistic insight into assembly of contractile nanomachines that bacteria and phages use to translocate macromolecules across membranes.
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Affiliation(s)
- Mikhail Kudryashev
- Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland; Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Ray Yu-Ruei Wang
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA; Graduate Program in Biological Physics, Structure and Design, University of Washington, Box 357350, Seattle, WA 98195, USA
| | - Maximilian Brackmann
- Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Sebastian Scherer
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Timm Maier
- Focal Area Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - David Baker
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA.
| | - Marek Basler
- Focal Area Infection Biology, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland.
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73
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The selective autophagy receptor p62 forms a flexible filamentous helical scaffold. Cell Rep 2015; 11:748-58. [PMID: 25921531 DOI: 10.1016/j.celrep.2015.03.062] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Revised: 02/22/2015] [Accepted: 03/24/2015] [Indexed: 12/24/2022] Open
Abstract
The scaffold protein p62/SQSTM1 is involved in protein turnover and signaling and is commonly found in dense protein bodies in eukaryotic cells. In autophagy, p62 acts as a selective autophagy receptor that recognizes and shuttles ubiquitinated proteins to the autophagosome for degradation. The structural organization of p62 in cellular bodies and the interplay of these assemblies with ubiquitin and the autophagic marker LC3 remain to be elucidated. Here, we present a cryo-EM structural analysis of p62. Together with structures of assemblies from the PB1 domain, we show that p62 is organized in flexible polymers with the PB1 domain constituting a helical scaffold. Filamentous p62 is capable of binding LC3 and addition of long ubiquitin chains induces disassembly and shortening of filaments. These studies explain how p62 assemblies provide a large molecular scaffold for the nascent autophagosome and reveal how they can bind ubiquitinated cargo.
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74
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Egelman EH. Three-dimensional reconstruction of helical polymers. Arch Biochem Biophys 2015; 581:54-8. [PMID: 25912526 DOI: 10.1016/j.abb.2015.04.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 04/06/2015] [Accepted: 04/14/2015] [Indexed: 11/18/2022]
Abstract
The field of three-dimensional electron microscopy began more than 45years ago with a reconstruction of a helical phage tail, and helical polymers continue to be important objects for three-dimensional reconstruction due to the centrality of helical protein and nucleoprotein polymers in all aspects of biology. We are now witnessing a fundamental revolution in this area, made possible by direct electron detectors, which has led to near-atomic resolution for a number of important helical structures. Most importantly, the possibility of achieving such resolution routinely for a vast number of helical samples is within our reach. One of the main problems in helical reconstruction, ambiguities in assigning the helical symmetry, is overcome when one reaches a resolution where secondary structure is clearly visible. However, obstacles still exist due to the intrinsic variability within many helical filaments.
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Affiliation(s)
- Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Box 800733, Charlottesville, VA 22908, USA.
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75
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Gutsche I, Desfosses A, Effantin G, Ling WL, Haupt M, Ruigrok RWH, Sachse C, Schoehn G. Structural virology. Near-atomic cryo-EM structure of the helical measles virus nucleocapsid. Science 2015; 348:704-7. [PMID: 25883315 DOI: 10.1126/science.aaa5137] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/06/2015] [Indexed: 01/25/2023]
Abstract
Measles is a highly contagious human disease. We used cryo-electron microscopy and single particle-based helical image analysis to determine the structure of the helical nucleocapsid formed by the folded domain of the measles virus nucleoprotein encapsidating an RNA at a resolution of 4.3 angstroms. The resulting pseudoatomic model of the measles virus nucleocapsid offers important insights into the mechanism of the helical polymerization of nucleocapsids of negative-strand RNA viruses, in particular via the exchange subdomains of the nucleoprotein. The structure reveals the mode of the nucleoprotein-RNA interaction and explains why each nucleoprotein of measles virus binds six nucleotides, whereas the respiratory syncytial virus nucleoprotein binds seven. It provides a rational basis for further analysis of measles virus replication and transcription, and reveals potential targets for drug design.
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Affiliation(s)
- Irina Gutsche
- CNRS, Unit for Virus Host-Cell Interactions, 38042 Grenoble, France. Université Grenoble Alpes, Unit for Virus Host-Cell Interactions, 38042 Grenoble, France.
| | - Ambroise Desfosses
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69917 Heidelberg, Germany
| | - Grégory Effantin
- CNRS, Unit for Virus Host-Cell Interactions, 38042 Grenoble, France. Université Grenoble Alpes, Unit for Virus Host-Cell Interactions, 38042 Grenoble, France
| | - Wai Li Ling
- Université Grenoble Alpes, IBS, 38044 Grenoble, France. CNRS, IBS, 38044 Grenoble, France. CEA, IBS, 38044 Grenoble, France
| | | | - Rob W H Ruigrok
- CNRS, Unit for Virus Host-Cell Interactions, 38042 Grenoble, France. Université Grenoble Alpes, Unit for Virus Host-Cell Interactions, 38042 Grenoble, France
| | - Carsten Sachse
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69917 Heidelberg, Germany
| | - Guy Schoehn
- CNRS, Unit for Virus Host-Cell Interactions, 38042 Grenoble, France. Université Grenoble Alpes, Unit for Virus Host-Cell Interactions, 38042 Grenoble, France. Université Grenoble Alpes, IBS, 38044 Grenoble, France. CNRS, IBS, 38044 Grenoble, France. CEA, IBS, 38044 Grenoble, France
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76
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Skruzny M, Desfosses A, Prinz S, Dodonova S, Gieras A, Uetrecht C, Jakobi A, Abella M, Hagen W, Schulz J, Meijers R, Rybin V, Briggs J, Sachse C, Kaksonen M. An Organized Co-assembly of Clathrin Adaptors Is Essential for Endocytosis. Dev Cell 2015; 33:150-62. [DOI: 10.1016/j.devcel.2015.02.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 11/29/2014] [Accepted: 02/25/2015] [Indexed: 10/23/2022]
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77
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Sachse C. Single-particle based helical reconstruction—how to make the most of real and Fourier space. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.2.219] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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78
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Fromm SA, Bharat TAM, Jakobi AJ, Hagen WJH, Sachse C. Seeing tobacco mosaic virus through direct electron detectors. J Struct Biol 2014; 189:87-97. [PMID: 25528571 PMCID: PMC4416312 DOI: 10.1016/j.jsb.2014.12.002] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/03/2014] [Accepted: 12/08/2014] [Indexed: 11/25/2022]
Abstract
With the introduction of direct electron detectors (DED) to the field of electron cryo-microscopy, a wave of atomic-resolution structures has become available. As the new detectors still require comparative characterization, we have used tobacco mosaic virus (TMV) as a test specimen to study the quality of 3D image reconstructions from data recorded on the two direct electron detector cameras, K2 Summit and Falcon II. Using DED movie frames, we explored related image-processing aspects and compared the performance of micrograph-based and segment-based motion correction approaches. In addition, we investigated the effect of dose deposition on the atomic-resolution structure of TMV and show that radiation damage affects negative carboxyl chains first in a side-chain specific manner. Finally, using 450,000 asymmetric units and limiting the effects of radiation damage, we determined a high-resolution cryo-EM map at 3.35 Å resolution. Here, we provide a comparative case study of highly ordered TMV recorded on different direct electron detectors to establish recording and processing conditions that enable structure determination up to 3.2 Å in resolution using cryo-EM.
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Affiliation(s)
- Simon A Fromm
- EMBL - European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Tanmay A M Bharat
- MRC Laboratory of Molecular Biology, Structural Studies Division, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Arjen J Jakobi
- EMBL - European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany; EMBL - European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 85, 22603 Hamburg, Germany
| | - Wim J H Hagen
- EMBL - European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany
| | - Carsten Sachse
- EMBL - European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.
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79
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Abstract
Helical polymers are found throughout biology and account for a substantial fraction
of the protein in a cell. These filaments are very attractive for three-dimensional
reconstruction from electron micrographs due to the fact that projections of these
filaments show many different views of identical subunits in identical environments.
However, ambiguities exist in defining the symmetry of a helical filament when one
has limited resolution, and mistakes can be made. Until one reaches a near-atomic
level of resolution, there are not necessarily reality-checks that can distinguish
between correct and incorrect solutions. A recent paper in eLife (Xu et al., 2014)
almost certainly imposed an incorrect helical symmetry and this can be seen using
filament images posted by Xu et al. A comparison between the atomic model proposed
and the published three-dimensional reconstruction should have suggested that an
incorrect solution was found. DOI:http://dx.doi.org/10.7554/eLife.04969.001
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Affiliation(s)
- Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, United States
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80
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Vahokoski J, Bhargav SP, Desfosses A, Andreadaki M, Kumpula EP, Martinez SM, Ignatev A, Lepper S, Frischknecht F, Sidén-Kiamos I, Sachse C, Kursula I. Structural differences explain diverse functions of Plasmodium actins. PLoS Pathog 2014; 10:e1004091. [PMID: 24743229 PMCID: PMC3990709 DOI: 10.1371/journal.ppat.1004091] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 03/11/2014] [Indexed: 11/18/2022] Open
Abstract
Actins are highly conserved proteins and key players in central processes in all eukaryotic cells. The two actins of the malaria parasite are among the most divergent eukaryotic actins and also differ from each other more than isoforms in any other species. Microfilaments have not been directly observed in Plasmodium and are presumed to be short and highly dynamic. We show that actin I cannot complement actin II in male gametogenesis, suggesting critical structural differences. Cryo-EM reveals that Plasmodium actin I has a unique filament structure, whereas actin II filaments resemble canonical F-actin. Both Plasmodium actins hydrolyze ATP more efficiently than α-actin, and unlike any other actin, both parasite actins rapidly form short oligomers induced by ADP. Crystal structures of both isoforms pinpoint several structural changes in the monomers causing the unique polymerization properties. Inserting the canonical D-loop to Plasmodium actin I leads to the formation of long filaments in vitro. In vivo, this chimera restores gametogenesis in parasites lacking actin II, suggesting that stable filaments are required for exflagellation. Together, these data underline the divergence of eukaryotic actins and demonstrate how structural differences in the monomers translate into filaments with different properties, implying that even eukaryotic actins have faced different evolutionary pressures and followed different paths for developing their polymerization properties. Malaria parasites have two actin isoforms, which are among the most divergent within the actin family that comprises highly conserved proteins, essential in all eukaryotic cells. In Plasmodium, actin is indispensable for motility and, thus, the infectivity of the deadly parasite. Yet, actin filaments have not been observed in vivo in these pathogens. Here, we show that the two Plasmodium actins differ from each other in both monomeric and filamentous form and that actin I cannot replace actin II during male gametogenesis. Whereas the major isoform actin I cannot form stable filaments alone, the mosquito-stage-specific actin II readily forms long filaments that have dimensions similar to canonical actins. A chimeric actin I mutant that forms long filaments in vitro also rescues gametogenesis in parasites lacking actin II. Both Plasmodium actins rapidly hydrolyze ATP and form short oligomers in the presence of ADP, which is a fundamental difference to all other actins characterized to date. Structural and functional differences in the two Plasmodium actin isoforms compared both to each other and to canonical actins reveal how the polymerization properties of eukaryotic actins have evolved along different avenues.
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Affiliation(s)
- Juha Vahokoski
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | | | - Ambroise Desfosses
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Maria Andreadaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology – Hellas, Heraklion, Crete, Greece
| | - Esa-Pekka Kumpula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Centre for Structural Systems Biology; Helmholtz Centre for Infection Research and German Electron Synchrotron, Hamburg, Germany
| | | | - Alexander Ignatev
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Simone Lepper
- Parasitology – Department of Infectious Diseases, University of Heidelberg Medical School, Heidelberg, Germany
| | - Friedrich Frischknecht
- Parasitology – Department of Infectious Diseases, University of Heidelberg Medical School, Heidelberg, Germany
| | - Inga Sidén-Kiamos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology – Hellas, Heraklion, Crete, Greece
| | - Carsten Sachse
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Inari Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- Centre for Structural Systems Biology; Helmholtz Centre for Infection Research and German Electron Synchrotron, Hamburg, Germany
- * E-mail:
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Rohou A, Grigorieff N. Frealix: model-based refinement of helical filament structures from electron micrographs. J Struct Biol 2014; 186:234-44. [PMID: 24657230 DOI: 10.1016/j.jsb.2014.03.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/12/2014] [Accepted: 03/13/2014] [Indexed: 12/20/2022]
Abstract
The structures of many helical protein filaments can be derived from electron micrographs of their suspensions in thin films of vitrified aqueous solutions. The most successful and generally-applicable approach treats short segments of these filaments as independent "single particles", yielding near-atomic resolution for rigid and well-ordered filaments. The single-particle approach can also accommodate filament deformations, yielding sub-nanometer resolution for more flexible filaments. However, in the case of thin and flexible filaments, such as some amyloid-β (Aβ) fibrils, the single-particle approach may fail because helical segments can be curved or otherwise distorted and their alignment can be inaccurate due to low contrast in the micrographs. We developed new software called Frealix that allows the use of arbitrarily short filament segments during alignment to approximate even high curvatures. All segments in a filament are aligned simultaneously with constraints that ensure that they connect to each other in space to form a continuous helical structure. In this paper, we describe the algorithm and benchmark it against datasets of Aβ(1-40) fibrils and tobacco mosaic virus (TMV), both analyzed in earlier work. In the case of TMV, our algorithm achieves similar results to single-particle analysis. In the case of Aβ(1-40) fibrils, we match the previously-obtained resolution but we are also able to obtain reliable alignments and ∼8-Å reconstructions from curved filaments. Our algorithm also offers a detailed characterization of filament deformations in three dimensions and enables a critical evaluation of the worm-like chain model for biological filaments.
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Affiliation(s)
- Alexis Rohou
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA
| | - Nikolaus Grigorieff
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA 02454, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
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