1
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Denisov N, Jannis D, Orekhov A, Müller-Caspary K, Verbeeck J. Characterization of a Timepix detector for use in SEM acceleration voltage range. Ultramicroscopy 2023; 253:113777. [PMID: 37336162 DOI: 10.1016/j.ultramic.2023.113777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Hybrid pixel direct electron detectors are gaining popularity in electron microscopy due to their excellent properties. Some commercial cameras based on this technology are relatively affordable which makes them attractive tools for experimentation especially in combination with an SEM setup. To support this, a detector characterization (Modulation Transfer Function, Detective Quantum Efficiency) of an Advacam Minipix and Advacam Advapix detector in the 15-30 keV range was made. In the current work we present images of Point Spread Function, plots of MTF/DQE curves and values of DQE(0) for these detectors. At low beam currents, the silicon detector layer behaviour should be dominant, which could make these findings transferable to any other available detector based on either Medipix2, Timepix or Timepix3 provided the same detector layer is used.
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Affiliation(s)
- Nikita Denisov
- EMAT, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
| | - Daen Jannis
- EMAT, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium
| | - Andrey Orekhov
- EMAT, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium
| | - Knut Müller-Caspary
- Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, Munich, 81377, Germany
| | - Johan Verbeeck
- EMAT, University of Antwerp, Groenenborgerlaan 171, Antwerp, 2020, Belgium.
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2
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Parasitology meets cryo-electron tomography – exciting prospects await. Trends Parasitol 2022; 38:365-378. [DOI: 10.1016/j.pt.2022.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 12/27/2022]
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3
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Ravikumar A, Gopnarayan MN, Subramaniam S, Srinivasan N. Comparison of side-chain dispersion in protein structures determined by cryo-EM and X-ray crystallography. IUCRJ 2022; 9:98-103. [PMID: 35059214 PMCID: PMC8733892 DOI: 10.1107/s2052252521011945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
An evaluation of systematic differences in local structure and conformation in the interior of protein tertiary structures determined by crystallography and by cryo-electron microscopy (cryo-EM) is reported. The expectation is that any consistent differences between the derived atomic models could provide insights into variations in side-chain packing that result from differences in specimens prepared for analysis between these two methods. By computing an atomic packing score, which provides a quantitative measure of clustering of side-chain atoms in the core of the tertiary structures, it is found that, in general, for structures determined by cryo-EM, side chains are more dispersed than in structures determined by X-ray crystallography over a similar resolution range. This trend is also observed in the packing comparison at subunit interfaces. Similar trends were observed in the packing comparison at the core of tertiary structures of the same proteins determined by both X-ray and cryo-EM methods. It is proposed here that the reduced dispersion of side chains in protein crystals could be due to some level of dehydration in 3D crystals prepared for X-ray crystallography and also because the higher rate of freezing of protein samples for cryo-EM may enable preservation of a more native conformation.
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Affiliation(s)
- Ashraya Ravikumar
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | | | - Sriram Subramaniam
- University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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4
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Liebschner D, Afonine PV, Moriarty NW, Poon BK, Chen VB, Adams PD. CERES: a cryo-EM re-refinement system for continuous improvement of deposited models. Acta Crystallogr D Struct Biol 2021; 77:48-61. [PMID: 33404525 PMCID: PMC7787109 DOI: 10.1107/s2059798320015879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/03/2020] [Indexed: 11/10/2022] Open
Abstract
The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM structures and how they might be improved, models deposited in the Protein Data Bank that have map resolutions of better than 5 Å were automatically re-refined using current versions of Phenix tools. The results are available on a publicly accessible web page (https://cci.lbl.gov/ceres). The implementation of a Cryo-EM Re-refinement System (CERES) for the improvement of models deposited in the wwPDB, and the results of the re-refinements, are described. Based on these results, contents are proposed for a `cryo-EM Table 1', which summarizes experimental details and validation metrics in a similar way to `Table 1' in crystallography. The consistent use of robust metrics for the evaluation of cryo-EM models and data should accompany every structure deposition and be reported in scientific publications.
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Affiliation(s)
- Dorothee Liebschner
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Pavel V. Afonine
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Nigel W. Moriarty
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Billy K. Poon
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Vincent B. Chen
- Department of Biochemistry, Duke University, Durham, NC 27710, USA
| | - Paul D. Adams
- Molecular Biosciences and Integrated Bioimaging, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
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5
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Birch J, Cheruvara H, Gamage N, Harrison PJ, Lithgo R, Quigley A. Changes in Membrane Protein Structural Biology. BIOLOGY 2020; 9:E401. [PMID: 33207666 PMCID: PMC7696871 DOI: 10.3390/biology9110401] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/21/2022]
Abstract
Membrane proteins are essential components of many biochemical processes and are important pharmaceutical targets. Membrane protein structural biology provides the molecular rationale for these biochemical process as well as being a highly useful tool for drug discovery. Unfortunately, membrane protein structural biology is a difficult area of study due to low protein yields and high levels of instability especially when membrane proteins are removed from their native environments. Despite this instability, membrane protein structural biology has made great leaps over the last fifteen years. Today, the landscape is almost unrecognisable. The numbers of available atomic resolution structures have increased 10-fold though advances in crystallography and more recently by cryo-electron microscopy. These advances in structural biology were achieved through the efforts of many researchers around the world as well as initiatives such as the Membrane Protein Laboratory (MPL) at Diamond Light Source. The MPL has helped, provided access to and contributed to advances in protein production, sample preparation and data collection. Together, these advances have enabled higher resolution structures, from less material, at a greater rate, from a more diverse range of membrane protein targets. Despite this success, significant challenges remain. Here, we review the progress made and highlight current and future challenges that will be overcome.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Harish Cheruvara
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadisha Gamage
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Peter J. Harrison
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Ryan Lithgo
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, Leicestershire, UK
| | - Andrew Quigley
- Membrane Protein Laboratory, Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; (J.B.); (H.C.); (N.G.); (P.J.H.); (R.L.)
- Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
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6
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Afonine PV, Klaholz BP, Moriarty NW, Poon BK, Sobolev OV, Terwilliger TC, Adams PD, Urzhumtsev A. New tools for the analysis and validation of cryo-EM maps and atomic models. Acta Crystallogr D Struct Biol 2018; 74:814-840. [PMID: 30198894 PMCID: PMC6130467 DOI: 10.1107/s2059798318009324] [Citation(s) in RCA: 479] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 06/27/2018] [Indexed: 11/25/2022] Open
Abstract
Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented in PHENIX are discussed, including d99 to estimate resolution, phenix.auto_sharpen to improve maps and phenix.mtriage to analyze cryo-EM maps. It is suggested that cryo-EM half-maps and masks should be deposited to facilitate the evaluation and validation of cryo-EM-derived atomic models and maps. The application of these tools to deposited cryo-EM atomic models and maps is also presented.
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Affiliation(s)
- Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Physics and International Centre for Quantum and Molecular Structures, Shanghai University, Shanghai, 200444, People’s Republic of China
| | - Bruno P. Klaholz
- Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Billy K. Poon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas C. Terwilliger
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- New Mexico Consortium, Los Alamos, NM 87544, USA
| | - Paul D. Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
| | - Alexandre Urzhumtsev
- Centre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS–INSERM–UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France
- Faculté des Sciences et Technologies, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy, France
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7
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Henderson R. Von der Elektronenkristallographie zur Einzelpartikel-KryoEM (Nobel-Aufsatz). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Richard Henderson
- MRC Laboratory of Molecular Biology; Francis Crick Avenue Cambridge CB2 0QH Großbritannien
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8
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Scapin G, Potter CS, Carragher B. Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application. Cell Chem Biol 2018; 25:1318-1325. [PMID: 30100349 DOI: 10.1016/j.chembiol.2018.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/11/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022]
Abstract
We present a perspective of our view of the application of cryoelectron microscopy (cryo-EM) to structure-based drug design (SBDD). We discuss the basic needs and requirements for SBDD, the current state of cryo-EM, and the challenges that need to be overcome for this technique to reach its full potential in facilitating the process of drug discovery.
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Affiliation(s)
- Giovanna Scapin
- Department of Biochemical Engineering & Structure, Merck & Co., Inc., 2000 Galloping Hill Rd., Kenilworth, NJ 07033, USA
| | - Clinton S Potter
- Simons Electron Microscopy Center, National Resource for Automated Molecular Microscopy, New York Structural Biology Center, 89 Convent Avenue, New York NY 10027, USA; NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, National Resource for Automated Molecular Microscopy, New York Structural Biology Center, 89 Convent Avenue, New York NY 10027, USA; NanoImaging Services, 4940 Carroll Canyon Road, Suite 115, San Diego, CA 92121, USA.
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9
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Henderson R. From Electron Crystallography to Single Particle CryoEM (Nobel Lecture). Angew Chem Int Ed Engl 2018; 57:10804-10825. [PMID: 29984560 DOI: 10.1002/anie.201802731] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Indexed: 01/08/2023]
Abstract
Pictures are a key to knowledge: The development of electron microscopy from its beginnings to modern single particle cryo-EM is described by R. Henderson in his Nobel lecture. Shown is the first projection structure at 7 Å resolution of the purple membrane from October 1974.
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Affiliation(s)
- Richard Henderson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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10
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Subramaniam S, Earl LA, Falconieri V, Milne JL, Egelman EH. Resolution advances in cryo-EM enable application to drug discovery. Curr Opin Struct Biol 2016; 41:194-202. [PMID: 27552081 DOI: 10.1016/j.sbi.2016.07.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 12/23/2022]
Abstract
The prospect that the structures of protein assemblies, small and large, can be determined using cryo-electron microscopy (cryo-EM) is beginning to transform the landscape of structural biology and cell biology. Great progress is being made in determining 3D structures of biological assemblies ranging from icosahedral viruses and helical arrays to small membrane proteins and protein complexes. Here, we review recent advances in this field, focusing especially on the emerging use of cryo-EM in mapping the binding of drugs and inhibitors to protein targets, an application that requires structure determination at the highest possible resolutions. We discuss methods used to evaluate the information contained in cryo-EM density maps and consider strengths and weaknesses of approaches currently used to measure map resolution.
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Affiliation(s)
- Sriram Subramaniam
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Lesley A Earl
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Veronica Falconieri
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jacqueline Ls Milne
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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11
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Affiliation(s)
- Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia.
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12
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Tate MW, Purohit P, Chamberlain D, Nguyen KX, Hovden R, Chang CS, Deb P, Turgut E, Heron JT, Schlom DG, Ralph DC, Fuchs GD, Shanks KS, Philipp HT, Muller DA, Gruner SM. High Dynamic Range Pixel Array Detector for Scanning Transmission Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2016; 22:237-49. [PMID: 26750260 DOI: 10.1017/s1431927615015664] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We describe a hybrid pixel array detector (electron microscope pixel array detector, or EMPAD) adapted for use in electron microscope applications, especially as a universal detector for scanning transmission electron microscopy. The 128×128 pixel detector consists of a 500 µm thick silicon diode array bump-bonded pixel-by-pixel to an application-specific integrated circuit. The in-pixel circuitry provides a 1,000,000:1 dynamic range within a single frame, allowing the direct electron beam to be imaged while still maintaining single electron sensitivity. A 1.1 kHz framing rate enables rapid data collection and minimizes sample drift distortions while scanning. By capturing the entire unsaturated diffraction pattern in scanning mode, one can simultaneously capture bright field, dark field, and phase contrast information, as well as being able to analyze the full scattering distribution, allowing true center of mass imaging. The scattering is recorded on an absolute scale, so that information such as local sample thickness can be directly determined. This paper describes the detector architecture, data acquisition system, and preliminary results from experiments with 80-200 keV electron beams.
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Affiliation(s)
- Mark W Tate
- 1Laboratory of Atomic and Solid State Physics,Cornell University,Ithaca,NY 14853,USA
| | - Prafull Purohit
- 1Laboratory of Atomic and Solid State Physics,Cornell University,Ithaca,NY 14853,USA
| | - Darol Chamberlain
- 2Cornell High Energy Synchrotron Source (CHESS),Cornell University,Ithaca,NY 14853,USA
| | - Kayla X Nguyen
- 3School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | - Robert Hovden
- 3School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | | | - Pratiti Deb
- 4Physics Department,Cornell University,Ithaca,NY 14853,USA
| | - Emrah Turgut
- 3School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | - John T Heron
- 4Physics Department,Cornell University,Ithaca,NY 14853,USA
| | - Darrell G Schlom
- 5Department of Materials Science and Engineering,Cornell University,Ithaca,NY 14853,USA
| | - Daniel C Ralph
- 1Laboratory of Atomic and Solid State Physics,Cornell University,Ithaca,NY 14853,USA
| | - Gregory D Fuchs
- 3School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | - Katherine S Shanks
- 1Laboratory of Atomic and Solid State Physics,Cornell University,Ithaca,NY 14853,USA
| | - Hugh T Philipp
- 1Laboratory of Atomic and Solid State Physics,Cornell University,Ithaca,NY 14853,USA
| | - David A Muller
- 3School of Applied and Engineering Physics,Cornell University,Ithaca,NY 14853,USA
| | - Sol M Gruner
- 1Laboratory of Atomic and Solid State Physics,Cornell University,Ithaca,NY 14853,USA
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13
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Clough R, Kirkland A. Direct Digital Electron Detectors. ADVANCES IN IMAGING AND ELECTRON PHYSICS 2016. [DOI: 10.1016/bs.aiep.2016.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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14
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Kuijper M, van Hoften G, Janssen B, Geurink R, De Carlo S, Vos M, van Duinen G, van Haeringen B, Storms M. FEI’s direct electron detector developments: Embarking on a revolution in cryo-TEM. J Struct Biol 2015; 192:179-87. [DOI: 10.1016/j.jsb.2015.09.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 09/23/2015] [Accepted: 09/25/2015] [Indexed: 10/23/2022]
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15
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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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16
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Faruqi A, Henderson R, McMullan G. Progress and Development of Direct Detectors for Electron Cryomicroscopy. ADVANCES IN IMAGING AND ELECTRON PHYSICS 2015. [DOI: 10.1016/bs.aiep.2015.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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17
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Abstract
Electron microscopy (EM) is an important tool for high-resolution structure determination in applications ranging from condensed matter to biology. Electronic detectors are now used in most applications in EM as they offer convenience and immediate feedback that is not possible with film or image plates. The earliest forms of electronic detector used routinely in transmission electron microscopy (TEM) were charge coupled devices (CCDs) and for many applications these remain perfectly adequate. There are however applications, such as the study of radiation-sensitive biological samples, where film is still used and improved detectors would be of great value. The emphasis in this review is therefore on detectors for use in such applications. Two of the most promising candidates for improved detection are: monolithic active pixel sensors (MAPS) and hybrid pixel detectors (of which Medipix2 was chosen for this study). From the studies described in this review, a back-thinned MAPS detector appears well suited to replace film in for the study of radiation-sensitive samples at 300 keV, while Medipix2 is suited to use at lower energies and especially in situations with very low count rates. The performance of a detector depends on the energy of electrons to be recorded, which in turn is dependent on the application it is being used for; results are described for a wide range of electron energies ranging from 40 to 300 keV. The basic properties of detectors are discussed in terms of their modulation transfer function (MTF) and detective quantum efficiency (DQE) as a function of spatial frequency.
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18
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Vulovic M, Rieger B, van Vliet LJ, Koster AJ, Ravelli RBG. A toolkit for the characterization of CCD cameras for transmission electron microscopy. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 66:97-109. [PMID: 20057054 DOI: 10.1107/s0907444909031205] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Accepted: 08/06/2009] [Indexed: 11/10/2022]
Abstract
Charge-coupled devices (CCD) are nowadays commonly utilized in transmission electron microscopy (TEM) for applications in life sciences. Direct access to digitized images has revolutionized the use of electron microscopy, sparking developments such as automated collection of tomographic data, focal series, random conical tilt pairs and ultralarge single-particle data sets. Nevertheless, for ultrahigh-resolution work photographic plates are often still preferred. In the ideal case, the quality of the recorded image of a vitrified biological sample would solely be determined by the counting statistics of the limited electron dose the sample can withstand before beam-induced alterations dominate. Unfortunately, the image is degraded by the non-ideal point-spread function of the detector, as a result of a scintillator coupled by fibre optics to a CCD, and the addition of several inherent noise components. Different detector manufacturers provide different types of figures of merit when advertising the quality of their detector. It is hard for most laboratories to verify whether all of the anticipated specifications are met. In this report, a set of algorithms is presented to characterize on-axis slow-scan large-area CCD-based TEM detectors. These tools have been added to a publicly available image-processing toolbox for MATLAB. Three in-house CCD cameras were carefully characterized, yielding, among others, statistics for hot and bad pixels, the modulation transfer function, the conversion factor, the effective gain and the detective quantum efficiency. These statistics will aid data-collection strategy programs and provide prior information for quantitative imaging. The relative performance of the characterized detectors is discussed and a comparison is made with similar detectors that are used in the field of X-ray crystallography.
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Affiliation(s)
- M Vulovic
- Section Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
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Faruqi AR. Principles and prospects of direct high resolution electron image acquisition with CMOS detectors at low energies. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:314004. [PMID: 21828565 DOI: 10.1088/0953-8984/21/31/314004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Two types of direct electron detectors, potentially useful in low energy electron microscopy and photoemission electron microscopy (LEEM/PEEM) experiments, are reviewed in this paper. Hybrid pixel detectors, using a silicon sensor and based on Medipix2 offer a high detective quantum efficiency, due to an essentially noiseless readout, but are technically challenging. Backthinned monolithic active pixel sensors (MAPS) are not noise-free but have other advantages as discussed in this review.
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Affiliation(s)
- A R Faruqi
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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Downing KH, Mooney PE. A charge coupled device camera with electron decelerator for intermediate voltage electron microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2008; 79:043702. [PMID: 18447528 PMCID: PMC2678785 DOI: 10.1063/1.2902853] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2008] [Accepted: 03/06/2008] [Indexed: 05/26/2023]
Abstract
Electron microscopists are increasingly turning to intermediate voltage electron microscopes (IVEMs) operating at 300-400 kV for a wide range of studies. They are also increasingly taking advantage of slow-scan charge coupled device (CCD) cameras, which have become widely used on electron microscopes. Under some conditions, CCDs provide an improvement in data quality over photographic film, as well as the many advantages of direct digital readout. However, CCD performance is seriously degraded on IVEMs compared to the more conventional 100 kV microscopes. In order to increase the efficiency and quality of data recording on IVEMs, we have developed a CCD camera system in which the electrons are decelerated to below 100 kV before impacting the camera, resulting in greatly improved performance in both signal quality and resolution compared to other CCDs used in electron microscopy. These improvements will allow high-quality image and diffraction data to be collected directly with the CCD, enabling improvements in data collection for applications including high-resolution electron crystallography, single particle reconstruction of protein structures, tomographic studies of cell ultrastructure, and remote microscope operation. This approach will enable us to use even larger format CCD chips that are being developed with smaller pixels.
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Affiliation(s)
- Kenneth H Downing
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
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McMullan G, Cattermole DM, Chen S, Henderson R, Llopart X, Summerfield C, Tlustos L, Faruqi AR. Electron imaging with Medipix2 hybrid pixel detector. Ultramicroscopy 2007; 107:401-13. [PMID: 17140733 DOI: 10.1016/j.ultramic.2006.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2006] [Revised: 10/04/2006] [Accepted: 10/17/2006] [Indexed: 11/17/2022]
Abstract
The electron imaging performance of Medipix2 is described. Medipix2 is a hybrid pixel detector composed of two layers. It has a sensor layer and a layer of readout electronics, in which each 55 microm x 55 microm pixel has upper and lower energy discrimination and MHz rate counting. The sensor layer consists of a 300 microm slab of pixellated monolithic silicon and this is bonded to the readout chip. Experimental measurement of the detective quantum efficiency, DQE(0) at 120 keV shows that it can reach approximately 85% independent of electron exposure, since the detector has zero noise, and the DQE(Nyquist) can reach approximately 35% of that expected for a perfect detector (4/pi(2)). Experimental measurement of the modulation transfer function (MTF) at Nyquist resolution for 120 keV electrons using a 60 keV lower energy threshold, yields a value that is 50% of that expected for a perfect detector (2/pi). Finally, Monte Carlo simulations of electron tracks and energy deposited in adjacent pixels have been performed and used to calculate expected values for the MTF and DQE as a function of the threshold energy. The good agreement between theory and experiment allows suggestions for further improvements to be made with confidence. The present detector is already very useful for experiments that require a high DQE at very low doses.
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Affiliation(s)
- G McMullan
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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Typke D, Gilpin CJ, Downing KH, Glaeser RM. Stroboscopic image capture: Reducing the dose per frame by a factor of 30 does not prevent beam-induced specimen movement in paraffin. Ultramicroscopy 2007; 107:106-15. [PMID: 16905258 DOI: 10.1016/j.ultramic.2006.06.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2005] [Revised: 05/31/2006] [Accepted: 06/07/2006] [Indexed: 11/30/2022]
Abstract
Beam-induced specimen movement may be the major factor that limits the quality of high-resolution images of organic specimens. One of the possible measures to improve the situation that was proposed by Henderson and Glaeser [Ultramicroscopy 16 (1985) 139-150], which we refer to here as "stroboscopic image capture", is to divide the normal exposure into many successive frames, thus reducing the amount of electron exposure--and possibly the amount of beam-induced movement--per frame. The frames would then be aligned and summed. We have performed preliminary experiments on stroboscopic imaging using a 200-kV electron microscope that was equipped with a high dynamic range Charge-coupled device (CCD) camera for image recording and a liquid N2-cooled cryoholder. Single-layer paraffin crystals on carbon film were used as a test specimen. The ratio F(g)/F(0) of paraffin reflections, calculated from the images, serves as our criterion for the image quality. In the series that were evaluated, no significant improvement of the F(image)(g)/F(image)(0) ratio was found, even though the electron exposure per frame was reduced by a factor of 30. A frame-to-frame analysis of image distortions showed that considerable beam-induced movement had still occurred during each frame. In addition, the paraffin crystal lattice was observed to move relative to the supporting carbon film, a fact that cannot be explained as being an electron-optical effect caused by specimen charging. We conclude that a significant further reduction of the dose per frame (than was possible with this CCD detector) will be needed in order to test whether the frame-to-frame changes ultimately become small enough for stroboscopic image capture to show its potential.
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Affiliation(s)
- Dieter Typke
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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Faruqi A. Direct Electron Detectors for Electron Microscopy. ADVANCES IN IMAGING AND ELECTRON PHYSICS 2007. [DOI: 10.1016/s1076-5670(06)45002-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Xuong NH, Jin L, Kleinfelder S, Li S, Leblanc P, Duttweiler F, Bouwer JC, Peltier ST, Milazzo AC, Ellisman M. Future directions for camera systems in electron microscopy. Methods Cell Biol 2007; 79:721-39. [PMID: 17327181 DOI: 10.1016/s0091-679x(06)79028-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Nguyen-Huu Xuong
- University of California, San Diego, La Jolla, California 92093, USA
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Milazzo AC, Leblanc P, Duttweiler F, Jin L, Bouwer JC, Peltier S, Ellisman M, Bieser F, Matis HS, Wieman H, Denes P, Kleinfelder S, Xuong NH. Active pixel sensor array as a detector for electron microscopy. Ultramicroscopy 2005; 104:152-9. [PMID: 15890445 DOI: 10.1016/j.ultramic.2005.03.006] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Revised: 02/25/2005] [Accepted: 03/16/2005] [Indexed: 11/22/2022]
Abstract
A new high-resolution recording device for transmission electron microscopy (TEM) is urgently needed. Neither film nor CCD cameras are systems that allow for efficient 3-D high-resolution particle reconstruction. We tested an active pixel sensor (APS) array as a replacement device at 200, 300, and 400 keV using a JEOL JEM-2000 FX II and a JEM-4000 EX electron microscope. For this experiment, we used an APS prototype with an area of 64 x 64 pixels of 20 microm x 20 microm pixel pitch. Single-electron events were measured by using very low beam intensity. The histogram of the incident electron energy deposited in the sensor shows a Landau distribution at low energies, as well as unexpected events at higher absorbed energies. After careful study, we concluded that backscattering in the silicon substrate and re-entering the sensitive epitaxial layer a second time with much lower speed caused the unexpected events. Exhaustive simulation experiments confirmed the existence of these back-scattered electrons. For the APS to be usable, the back-scattered electron events must be eliminated, perhaps by thinning the substrate to less than 30 microm. By using experimental data taken with an APS chip with a standard silicon substrate (300 microm) and adjusting the results to take into account the effect of a thinned silicon substrate (30 microm), we found an estimate of the signal-to-noise ratio for a back-thinned detector in the energy range of 200-400 keV was about 10:1 and an estimate for the spatial resolution was about 10 microm.
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Affiliation(s)
- Anna-Clare Milazzo
- University of California at San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
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Abstract
Emerging techniques in electron microscopy promise to yield a wide range of new information about the nervous system. Aided by the development of detectors, electron optics, energy filters, computer automation and preparative methods, electron tomography now provides three-dimensional structures over a scale ranging from single receptor molecules to synapses and neurons. To relate structure to function, a variety of correlative methods are being developed, including protein tags observable both by light microscopy of living cells and, subsequently, by electron microscopy. It is also becoming possible to measure functionally important ions like Ca(2+) in cellular compartments at a scale of about 10 nm by exploiting new advances in electron energy loss and X-ray spectroscopic imaging.
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Affiliation(s)
- Richard D Leapman
- Division of Bioengineering and Physical Science, ORS, National Institutes of Health, Building 13, Room 3N17, 9000 Rockville Pike, Bethesda, Maryland 20982, USA.
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Zhang P, Borgnia MJ, Mooney P, Shi D, Pan M, O'Herron P, Mao A, Brogan D, Milne JLS, Subramaniam S. Automated image acquisition and processing using a new generation of 4K x 4K CCD cameras for cryo electron microscopic studies of macromolecular assemblies. J Struct Biol 2003; 143:135-44. [PMID: 12972350 DOI: 10.1016/s1047-8477(03)00124-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We have previously reported the development of AutoEM, a software package for semi-automated acquisition of data from a transmission electron microscope. In continuing efforts to improve the speed of structure determination of macromolecular assemblies by electron microscopy, we report here on the performance of a new generation of 4 K CCD cameras for use in cryo electron microscopic applications. We demonstrate that at 120 kV, and at a nominal magnification of 67000 x, power spectra and signal-to-noise ratios for the new 4 K CCD camera are comparable to values obtained for film images scanned using a Zeiss scanner to resolutions as high as approximately 1/6.5A(-1). The specimen area imaged for each exposure on the 4 K CCD is about one-third of the area that can be recorded with a similar exposure on film. The CCD camera also serves the purpose of recording images at low magnification from the center of the hole to measure the thickness of vitrified ice in the hole. The performance of the camera is satisfactory under the low-dose conditions used in cryo electron microscopy, as demonstrated here by the determination of a three-dimensional map at 15 A for the catalytic core of the 1.8 MDa Bacillus stearothermophilus icosahedral pyruvate dehydrogenase complex, and its comparison with the previously reported atomic model for this complex obtained by X-ray crystallography.
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Affiliation(s)
- Peijun Zhang
- Laboratory of Biochemistry, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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