1
|
Premageetha GT, Vinothkumar KR, Bose S. Exploring advances in single particle CryoEM with apoferritin: From blobs to true atomic resolution. Int J Biochem Cell Biol 2024; 169:106536. [PMID: 38307321 DOI: 10.1016/j.biocel.2024.106536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/21/2024] [Accepted: 01/23/2024] [Indexed: 02/04/2024]
Abstract
Deciphering the three-dimensional structures of macromolecules is of paramount importance for gaining insights into their functions and roles in human health and disease. Single particle cryoEM has emerged as a powerful technique that enables direct visualization of macromolecules and their complexes, and through subsequent averaging, achieve near atomic-level resolution. A major breakthrough was recently achieved with the determination of the apoferritin structure at true atomic resolution. In this review, we discuss the latest technological innovations across the entire single-particle workflow, which have been instrumental in driving the resolution revolution and in transforming cryoEM as a mainstream technique in structural biology. We illustrate these advancements using apoferritin as an example that has served as an excellent benchmark sample for assessing emerging technologies. We further explore whether the existing technology can routinely generate atomic structures of dynamic macromolecules that more accurately represent real-world samples, the limitations in the workflow, and the current approaches employed to overcome them.
Collapse
Affiliation(s)
- Gowtham ThambraRajan Premageetha
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bangalore 560065, India; Manipal Academy of Higher Education, Tiger Circle Road, Manipal, Karnataka 576104, India.
| | - Kutti R Vinothkumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Post, Bangalore 560065, India
| | - Sucharita Bose
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Post, Bangalore 560065, India.
| |
Collapse
|
2
|
Tani K, Kanno R, Harada A, Kobayashi Y, Minamino A, Takenaka S, Nakamura N, Ji XC, Purba ER, Hall M, Yu LJ, Madigan MT, Mizoguchi A, Iwasaki K, Humbel BM, Kimura Y, Wang-Otomo ZY. High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum. Commun Biol 2024; 7:176. [PMID: 38347078 PMCID: PMC10861460 DOI: 10.1038/s42003-024-05863-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
The mesophilic purple sulfur phototrophic bacterium Allochromatium (Alc.) vinosum (bacterial family Chromatiaceae) has been a favored model for studies of bacterial photosynthesis and sulfur metabolism, and its core light-harvesting (LH1) complex has been a focus of numerous studies of photosynthetic light reactions. However, despite intense efforts, no high-resolution structure and thorough biochemical analysis of the Alc. vinosum LH1 complex have been reported. Here we present cryo-EM structures of the Alc. vinosum LH1 complex associated with reaction center (RC) at 2.24 Å resolution. The overall structure of the Alc. vinosum LH1 resembles that of its moderately thermophilic relative Alc. tepidum in that it contains multiple pigment-binding α- and β-polypeptides. Unexpectedly, however, six Ca ions were identified in the Alc. vinosum LH1 bound to certain α1/β1- or α1/β3-polypeptides through a different Ca2+-binding motif from that seen in Alc. tepidum and other Chromatiaceae that contain Ca2+-bound LH1 complexes. Two water molecules were identified as additional Ca2+-coordinating ligands. Based on these results, we reexamined biochemical and spectroscopic properties of the Alc. vinosum LH1-RC. While modest but distinct effects of Ca2+ were detected in the absorption spectrum of the Alc. vinosum LH1 complex, a marked decrease in thermostability of its LH1-RC complex was observed upon removal of Ca2+. The presence of Ca2+ in the photocomplex of Alc. vinosum suggests that Ca2+-binding to LH1 complexes may be a common adaptation in species of Chromatiaceae for conferring spectral and thermal flexibility on this key component of their photosynthetic machinery.
Collapse
Affiliation(s)
- Kazutoshi Tani
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan.
- Graduate School of Medicine, Mie University, 1577 Kurimamachiyacho, Tsu, 514-8507, Japan.
| | - Ryo Kanno
- Quantum Wave Microscopy Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Ayaka Harada
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Yuki Kobayashi
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - Akane Minamino
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - Shinji Takenaka
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | | | - Xuan-Cheng Ji
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - Endang R Purba
- Scientific Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Malgorzata Hall
- Scientific Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Michael T Madigan
- School of Biological Sciences, Program in Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Akira Mizoguchi
- Graduate School of Medicine, Mie University, 1577 Kurimamachiyacho, Tsu, 514-8507, Japan
| | - Kenji Iwasaki
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Bruno M Humbel
- Provost Office, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
- Department of Cell Biology and Neuroscience, Juntendo University, Graduate School of Medicine, Tokyo, 113-8421, Japan
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan.
| | | |
Collapse
|
3
|
Pattison AJ, Pedroso CCS, Cohen BE, Ondry JC, Alivisatos AP, Theis W, Ercius P. Advanced techniques in automated high-resolution scanning transmission electron microscopy. NANOTECHNOLOGY 2023; 35:015710. [PMID: 37703845 DOI: 10.1088/1361-6528/acf938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 09/12/2023] [Indexed: 09/15/2023]
Abstract
Scanning transmission electron microscopy is a common tool used to study the atomic structure of materials. It is an inherently multimodal tool allowing for the simultaneous acquisition of multiple information channels. Despite its versatility, however, experimental workflows currently rely heavily on experienced human operators and can only acquire data from small regions of a sample at a time. Here, we demonstrate a flexible pipeline-based system for high-throughput acquisition of atomic-resolution structural data using an all-piezo sample stage applied to large-scale imaging of nanoparticles and multimodal data acquisition. The system is available as part of the user program of the Molecular Foundry at Lawrence Berkeley National Laboratory.
Collapse
Affiliation(s)
- Alexander J Pattison
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, United States of America
| | - Cassio C S Pedroso
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, United States of America
| | - Bruce E Cohen
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, United States of America
- Division of Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States of America
| | - Justin C Ondry
- Department of Chemistry, University of California, Berkeley, CA, United States of America
- Kavli Energy NanoScience Institute, Berkeley, CA, United States of America
- Department of Chemistry and Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, United States of America
| | - A Paul Alivisatos
- Department of Chemistry, University of California, Berkeley, CA, United States of America
- Kavli Energy NanoScience Institute, Berkeley, CA, United States of America
- Department of Chemistry and Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, United States of America
- Material Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Materials Science and Engineering, University of California, Berkeley, CA, United States of America
| | - Wolfgang Theis
- School of Physics and Astronomy, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Peter Ercius
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, United States of America
| |
Collapse
|
4
|
Cheng A, Kim PT, Kuang H, Mendez JH, Chua EYD, Maruthi K, Wei H, Sawh A, Aragon MF, Serbynovskyi V, Neselu K, Eng ET, Potter CS, Carragher B, Bepler T, Noble AJ. Fully automated multi-grid cryoEM screening using Smart Leginon. IUCRJ 2023; 10:77-89. [PMID: 36598504 PMCID: PMC9812217 DOI: 10.1107/s2052252522010624] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
Single-particle cryo-electron microscopy (cryoEM) is a swiftly growing method for understanding protein structure. With increasing demand for high-throughput, high-resolution cryoEM services comes greater demand for rapid and automated cryoEM grid and sample screening. During screening, optimal grids and sample conditions are identified for subsequent high-resolution data collection. Screening is a major bottleneck for new cryoEM projects because grids must be optimized for several factors, including grid type, grid hole size, sample concentration, buffer conditions, ice thickness and particle behavior. Even for mature projects, multiple grids are commonly screened to select a subset for high-resolution data collection. Here, machine learning and novel purpose-built image-processing and microscope-handling algorithms are incorporated into the automated data-collection software Leginon, to provide an open-source solution for fully automated high-throughput grid screening. This new version, broadly called Smart Leginon, emulates the actions of an operator in identifying areas on the grid to explore as potentially useful for data collection. Smart Leginon Autoscreen sequentially loads and examines grids from an automated specimen-exchange system to provide completely unattended grid screening across a set of grids. Comparisons between a multi-grid autoscreen session and conventional manual screening by 5 expert microscope operators are presented. On average, Autoscreen reduces operator time from ∼6 h to <10 min and provides a percentage of suitable images for evaluation comparable to the best operator. The ability of Smart Leginon to target holes that are particularly difficult to identify is analyzed. Finally, the utility of Smart Leginon is illustrated with three real-world multi-grid user screening/collection sessions, demonstrating the efficiency and flexibility of the software package. The fully automated functionality of Smart Leginon significantly reduces the burden on operator screening time, improves the throughput of screening and recovers idle microscope time, thereby improving availability of cryoEM services.
Collapse
Affiliation(s)
- Anchi Cheng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Paul T. Kim
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| | - Huihui Kuang
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Joshua H. Mendez
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Eugene Y. D. Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Kashyap Maruthi
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Hui Wei
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Anjelique Sawh
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Mahira F. Aragon
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | | | - Kasahun Neselu
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Clinton S. Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Tristan Bepler
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| | - Alex J. Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Simons Machine Learning Center, New York Structural Biology Center, New York, NY, USA
| |
Collapse
|
5
|
DiIorio MC, Kulczyk AW. Exploring the Structural Variability of Dynamic Biological Complexes by Single-Particle Cryo-Electron Microscopy. MICROMACHINES 2022; 14:mi14010118. [PMID: 36677177 PMCID: PMC9866264 DOI: 10.3390/mi14010118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 12/27/2022] [Accepted: 12/30/2022] [Indexed: 05/15/2023]
Abstract
Biological macromolecules and assemblies precisely rearrange their atomic 3D structures to execute cellular functions. Understanding the mechanisms by which these molecular machines operate requires insight into the ensemble of structural states they occupy during the functional cycle. Single-particle cryo-electron microscopy (cryo-EM) has become the preferred method to provide near-atomic resolution, structural information about dynamic biological macromolecules elusive to other structure determination methods. Recent advances in cryo-EM methodology have allowed structural biologists not only to probe the structural intermediates of biochemical reactions, but also to resolve different compositional and conformational states present within the same dataset. This article reviews newly developed sample preparation and single-particle analysis (SPA) techniques for high-resolution structure determination of intrinsically dynamic and heterogeneous samples, shedding light upon the intricate mechanisms employed by molecular machines and helping to guide drug discovery efforts.
Collapse
Affiliation(s)
- Megan C. DiIorio
- Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Arkadiusz W. Kulczyk
- Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, USA
- Department of Biochemistry and Microbiology, Rutgers University, 75 Lipman Drive, New Brunswick, NJ 08901, USA
- Correspondence:
| |
Collapse
|
6
|
Burley SK, Berman HM, Chiu W, Dai W, Flatt JW, Hudson BP, Kaelber JT, Khare SD, Kulczyk AW, Lawson CL, Pintilie GD, Sali A, Vallat B, Westbrook JD, Young JY, Zardecki C. Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future. Biophys Rev 2022; 14:1281-1301. [PMID: 36474933 PMCID: PMC9715422 DOI: 10.1007/s12551-022-01013-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/06/2022] [Indexed: 12/04/2022] Open
Abstract
As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) "Resolution Revolution" made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.
Collapse
Affiliation(s)
- Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093 USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Wah Chiu
- Department of Bioengineering, Stanford University, Stanford, CA USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA USA
| | - Wei Dai
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Justin W. Flatt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Brian P. Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Jason T. Kaelber
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 174 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Arkadiusz W. Kulczyk
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08901 USA
| | - Catherine L. Lawson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | | | - Andrej Sali
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158 USA
| | - Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
| | - John D. Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901 USA
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| |
Collapse
|
7
|
Bepler T, Borst AJ, Bouvette J, Cannone G, Chen S, Cheng A, Cheng A, Fan Q, Grollios F, Gupta H, Gupta M, Humphreys T, Kim PT, Kuang H, Li Y, Noble AJ, Punjani A, Rice WJ, Oscar S Sorzano C, Stagg SM, Strauss J, Yu L, Carragher B, Potter CS. Smart data collection for CryoEM. J Struct Biol 2022; 214:107913. [PMID: 36341954 DOI: 10.1016/j.jsb.2022.107913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/29/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
Abstract
This report provides an overview of the discussions, presentations, and consensus thinking from the Workshop on Smart Data Collection for CryoEM held at the New York Structural Biology Center on April 6-7, 2022. The goal of the workshop was to address next generation data collection strategies that integrate machine learning and real-time processing into the workflow to reduce or eliminate the need for operator intervention.
Collapse
Affiliation(s)
| | - Andrew J Borst
- University of Washington, Institute for Protein Design, Seattle, WA, USA
| | - Jonathan Bouvette
- National Institute of Environmental Health Sciences, NIH, Durham, NC, USA
| | - Giuseppe Cannone
- Laboratory for Molecular Biology, Medical Research Council, Cambridge, England
| | - Songye Chen
- California Institute of Technology, Pasadena, CA, USA
| | - Anchi Cheng
- New York Structural Biology Center, New York, NY, USA
| | - Ao Cheng
- Northwestern University, Evanston, IL, USA
| | - Quanfu Fan
- MIT-IBM Watson AI Lab, Cambridge, MA, USA
| | | | - Harshit Gupta
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Meghna Gupta
- University of California at San Francisco, San Francisco, CA, USA
| | | | - Paul T Kim
- New York Structural Biology Center, New York, NY, USA
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, USA
| | - Yilai Li
- University of Michigan, Ann Arbor, MI, USA
| | - Alex J Noble
- New York Structural Biology Center, New York, NY, USA
| | | | - William J Rice
- New York University School of Medicine, New York, NY, USA
| | | | | | - Joshua Strauss
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lingbo Yu
- ThermoFisher Scientific, Eindhoven, The Netherlands
| | | | | |
Collapse
|
8
|
Gerle C, Kishikawa JI, Yamaguchi T, Nakanishi A, Çoruh O, Makino F, Miyata T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. Structures of Multisubunit Membrane Complexes With the CRYO ARM 200. Microscopy (Oxf) 2022; 71:249-261. [PMID: 35861182 PMCID: PMC9535789 DOI: 10.1093/jmicro/dfac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 11/18/2022] Open
Abstract
Progress in structural membrane biology has been significantly accelerated by the ongoing ‘Resolution Revolution’ in cryo-electron microscopy (cryo-EM). In particular, structure determination by single-particle analysis has evolved into the most powerful method for atomic model building of multisubunit membrane protein complexes. This has created an ever-increasing demand in cryo-EM machine time, which to satisfy is in need of new and affordable cryo-electron microscopes. Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the structure determination by single-particle analysis of three different multisubunit membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus elongatus photosystem I monomer and the flagellar motor lipopolysaccharide peptidoglycan ring (LP ring) from Salmonella enterica.
Collapse
Affiliation(s)
- Christoph Gerle
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan.,RIKEN SPring-8 Center, Life Science Research Infrastructure Group, Sayo-gun, Hyogo 679-5148, Japan
| | - Jun-Ichi Kishikawa
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan
| | - Tomoko Yamaguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Atsuko Nakanishi
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan.,Research Center for Ultra-High Voltage Electron Microscopy, Osaka, University, Ibaraki, Osaka 567-0047, Japan
| | - Orkun Çoruh
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan.,Institute of Science and Technology Austria, Klosterneuburg, 3400 Austria
| | - Fumiaki Makino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,JEOL Ltd., Akishima, Tokyo, Japan
| | - Tomoko Miyata
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan
| | - Ken Yokoyama
- Department of Molecular Biosciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kyoto, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,RIKEN Center for Biosystems Dynamics Research, Suita, Osaka, Japan.,JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, 3-2 Yamada Oka, Suita, Osaka 565-0871, Japan.,Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| |
Collapse
|
9
|
Chua EYD, Mendez JH, Rapp M, Ilca SL, Tan YZ, Maruthi K, Kuang H, Zimanyi CM, Cheng A, Eng ET, Noble AJ, Potter CS, Carragher B. Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy. Annu Rev Biochem 2022; 91:1-32. [PMID: 35320683 PMCID: PMC10393189 DOI: 10.1146/annurev-biochem-032620-110705] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cryo-electron microscopy (cryo-EM) continues its remarkable growth as a method for visualizing biological objects, which has been driven by advances across the entire pipeline. Developments in both single-particle analysis and in situ tomography have enabled more structures to be imaged and determined to better resolutions, at faster speeds, and with more scientists having improved access. This review highlights recent advances at each stageof the cryo-EM pipeline and provides examples of how these techniques have been used to investigate real-world problems, including antibody development against the SARS-CoV-2 spike during the recent COVID-19 pandemic.
Collapse
Affiliation(s)
- Eugene Y D Chua
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Joshua H Mendez
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Micah Rapp
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Serban L Ilca
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, Singapore;
- Disease Intervention Technology Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kashyap Maruthi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Christina M Zimanyi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Anchi Cheng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Edward T Eng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Alex J Noble
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Clinton S Potter
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Bridget Carragher
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| |
Collapse
|
10
|
Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome. Nat Commun 2022; 13:3389. [PMID: 35715389 PMCID: PMC9205905 DOI: 10.1038/s41467-022-30962-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 05/24/2022] [Indexed: 11/21/2022] Open
Abstract
Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are compositionally and structurally diverse, and exceedingly complex, all of which pose a challenge for a comprehensive understanding of their function. To date, three detailed architectures of PBSs by cryo-electron microscopy (cryo-EM) have been described: a hemiellipsoidal type, a block-type from rhodophytes, and a cyanobacterial hemidiscoidal-type. Here, we report cryo-EM structures of a pentacylindrical allophycocyanin core and phycocyanin-containing rod of a thermophilic cyanobacterial hemidiscoidal PBS. The structures define the spatial arrangement of protein subunits and chromophores, crucial for deciphering the energy transfer mechanism. They reveal how the pentacylindrical core is formed, identify key interactions between linker proteins and the bilin chromophores, and indicate pathways for unidirectional energy transfer. Phycobilisome (PBS) absorbs solar energy and transfer the energy to photosynthetic membrane proteins. In this study, the structures of the pentacylindrical core and rod in PBS from a thermophilic cyanobacterium by cryo-electron microscopy.
Collapse
|
11
|
Tani K, Kobayashi K, Hosogi N, Ji XC, Nagashima S, Nagashima KVP, Izumida A, Inoue K, Tsukatani Y, Kanno R, Hall M, Yu LJ, Ishikawa I, Okura Y, Madigan MT, Mizoguchi A, Humbel BM, Kimura Y, Wang-Otomo ZY. A Ca 2+-binding motif underlies the unusual properties of certain photosynthetic bacterial core light-harvesting complexes. J Biol Chem 2022; 298:101967. [PMID: 35460693 PMCID: PMC9133646 DOI: 10.1016/j.jbc.2022.101967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 01/24/2023] Open
Abstract
The mildly thermophilic purple phototrophic bacterium Allochromatium tepidum provides a unique model for investigating various intermediate phenotypes observed between those of thermophilic and mesophilic counterparts. The core light-harvesting (LH1) complex from A. tepidum exhibits an absorption maximum at 890 nm and mildly enhanced thermostability, both of which are Ca2+-dependent. However, it is unknown what structural determinants might contribute to these properties. Here, we present a cryo-EM structure of the reaction center–associated LH1 complex at 2.81 Å resolution, in which we identify multiple pigment-binding α- and β-polypeptides within an LH1 ring. Of the 16 α-polypeptides, we show that six (α1) bind Ca2+ along with β1- or β3-polypeptides to form the Ca2+-binding sites. This structure differs from that of fully Ca2+-bound LH1 from Thermochromatium tepidum, enabling determination of the minimum structural requirements for Ca2+-binding. We also identified three amino acids (Trp44, Asp47, and Ile49) in the C-terminal region of the A. tepidum α1-polypeptide that ligate each Ca ion, forming a Ca2+-binding WxxDxI motif that is conserved in all Ca2+-bound LH1 α-polypeptides from other species with reported structures. The partial Ca2+-bound structure further explains the unusual phenotypic properties observed for this bacterium in terms of its Ca2+-requirements for thermostability, spectroscopy, and phototrophic growth, and supports the hypothesis that A. tepidum may represent a “transitional” species between mesophilic and thermophilic purple sulfur bacteria. The characteristic arrangement of multiple αβ-polypeptides also suggests a mechanism of molecular recognition in the expression and/or assembly of the LH1 complex that could be regulated through interactions with reaction center subunits.
Collapse
Affiliation(s)
- Kazutoshi Tani
- Graduate School of Medicine, Mie University, Tsu, Japan.
| | - Kazumi Kobayashi
- EM Business Unit, JEOL Ltd 3-1-2 Musashino, Akishima, Tokyo, Japan
| | - Naoki Hosogi
- EM Business Unit, JEOL Ltd 3-1-2 Musashino, Akishima, Tokyo, Japan
| | | | - Sakiko Nagashima
- Research Institute for Integrated Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
| | - Kenji V P Nagashima
- Research Institute for Integrated Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
| | - Airi Izumida
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
| | - Kazuhito Inoue
- Research Institute for Integrated Science, Kanagawa University, Hiratsuka, Kanagawa, Japan; Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Kanagawa, Japan
| | - Yusuke Tsukatani
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa, Japan
| | - Ryo Kanno
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), Kunigami-gun, Okinawa, Japan
| | - Malgorzata Hall
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), Kunigami-gun, Okinawa, Japan
| | - Long-Jiang Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Isamu Ishikawa
- EM Business Unit, JEOL Ltd 3-1-2 Musashino, Akishima, Tokyo, Japan
| | - Yoshihiro Okura
- EM Business Unit, JEOL Ltd 3-1-2 Musashino, Akishima, Tokyo, Japan
| | - Michael T Madigan
- School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, Illinois, USA
| | | | - Bruno M Humbel
- Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), Kunigami-gun, Okinawa, Japan
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, Japan.
| | | |
Collapse
|
12
|
Machine learning-based real-time object locator/evaluator for cryo-EM data collection. Commun Biol 2021; 4:1044. [PMID: 34493805 PMCID: PMC8423793 DOI: 10.1038/s42003-021-02577-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/20/2021] [Indexed: 11/30/2022] Open
Abstract
In cryo-electron microscopy (cryo-EM) data collection, locating a target object is error-prone. Here, we present a machine learning-based approach with a real-time object locator named yoneoLocr using YOLO, a well-known object detection system. Implementation shows its effectiveness in rapidly and precisely locating carbon holes in single particle cryo-EM and in locating crystals and evaluating electron diffraction (ED) patterns in automated cryo-electron crystallography (cryo-EX) data collection. The proposed approach will advance high-throughput and accurate data collection of images and diffraction patterns with minimal human operation. Yonekura et al. present yoneoLocr, a machine learning-based real-time object locator for rapidly and precisely locating carbon holes and crystals for facilitating automated SPA or cryo-EX data collection.
Collapse
|
13
|
Yu H, Hamaguchi T, Nakajima Y, Kato K, Kawakami K, Akita F, Yonekura K, Shen JR. Cryo-EM structure of monomeric photosystem II at 2.78 Å resolution reveals factors important for the formation of dimer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148471. [PMID: 34216574 DOI: 10.1016/j.bbabio.2021.148471] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 06/18/2021] [Accepted: 06/26/2021] [Indexed: 11/29/2022]
Abstract
Photosystem II (PSII) functions mainly as a dimer to catalyze the light energy conversion and water oxidation reactions. However, monomeric PSII also exists and functions in vivo in some cases. The crystal structure of monomeric PSII has been solved at 3.6 Å resolution, but it is still not clear which factors contribute to the formation of the dimer. Here, we solved the structure of PSII monomer at a resolution of 2.78 Å using cryo-electron microscopy (cryo-EM). From our cryo-EM density map, we observed apparent differences in pigments and lipids in the monomer-monomer interface between the PSII monomer and dimer. One β-carotene and two sulfoquinovosyl diacylglycerol (SQDG) molecules are found in the monomer-monomer interface of the dimer structure but not in the present monomer structure, although some SQDG and other lipid molecules are found in the analogous region of the low-resolution crystal structure of the monomer, or cryo-EM structure of an apo-PSII monomer lacking the extrinsic proteins from Synechocystis sp. PCC 6803. In the current monomer structure, a large part of the PsbO subunit was also found to be disordered. These results indicate the importance of the β-carotene, SQDG and PsbO in formation of the PSII dimer.
Collapse
Affiliation(s)
- Huaxin Yu
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan; Department of Picobiology, Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Yoshiki Nakajima
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Koji Kato
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan
| | - Keisuke Kawakami
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Fusamichi Akita
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan; Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan; Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.
| | - Jian-Ren Shen
- Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan.
| |
Collapse
|
14
|
Hamaguchi T, Kawakami K, Shinzawa-Itoh K, Inoue-Kashino N, Itoh S, Ifuku K, Yamashita E, Maeda K, Yonekura K, Kashino Y. Structure of the far-red light utilizing photosystem I of Acaryochloris marina. Nat Commun 2021; 12:2333. [PMID: 33879791 PMCID: PMC8058080 DOI: 10.1038/s41467-021-22502-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 03/18/2021] [Indexed: 01/09/2023] Open
Abstract
Acaryochloris marina is one of the cyanobacterial species that can use far-red light to drive photochemical reactions for oxygenic photosynthesis. Here, we report the structure of A. marina photosystem I (PSI) reaction center, determined by cryo-electron microscopy at 2.58 Å resolution. The structure reveals an arrangement of electron carriers and light-harvesting pigments distinct from other type I reaction centers. The paired chlorophyll, or special pair (also referred to as P740 in this case), is a dimer of chlorophyll d and its epimer chlorophyll d'. The primary electron acceptor is pheophytin a, a metal-less chlorin. We show the architecture of this PSI reaction center is composed of 11 subunits and we identify key components that help explain how the low energy yield from far-red light is efficiently utilized for driving oxygenic photosynthesis.
Collapse
Affiliation(s)
- Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Hyogo, Japan
| | - Keisuke Kawakami
- Research Center for Artificial Photosynthesis (ReCAP), Osaka City University, Sumiyoshi-ku, Osaka, Japan.
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Hyogo, Japan.
| | | | | | - Shigeru Itoh
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kentaro Ifuku
- Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Eiki Yamashita
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kou Maeda
- Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Hyogo, Japan.
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba-ku, Sendai, Japan.
| | - Yasuhiro Kashino
- Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo, Japan.
| |
Collapse
|
15
|
Maki-Yonekura S, Hamaguchi T, Naitow H, Takaba K, Yonekura K. Advances in cryo-EM and ED with a cold-field emission beam and energy filtration -Refinements of the CRYO ARM 300 system in RIKEN SPring-8 center. Microscopy (Oxf) 2021; 70:232-240. [PMID: 33245780 DOI: 10.1093/jmicro/dfaa052] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/26/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
We have designed and evaluated a cryo-electron microscopy (cryo-EM) system for higher-resolution single particle analysis and high-precision electron 3D crystallography. The system comprises a JEOL CRYO ARM 300 electron microscope-the first machine of this model-and a direct detection device camera, a scintillator-coupled camera, GPU clusters connected with a camera control computer and software for automated-data collection and efficient and accurate operation. The microscope provides parallel illumination of a highly coherent 300-kV electron beam to a sample from a cold-field emission gun and filters out energy-loss electrons through the sample with an in-column energy filter. The gun and filter are highly effective in improving imaging and diffraction, respectively, and have provided high quality data since July 2018. We here report on the characteristics of the cryo-EM system, updates, our progress and future plan for running such cryo-EM machines in RIKEN SPring-8 Center.
Collapse
Affiliation(s)
- Saori Maki-Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Hisashi Naitow
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Kiyofumi Takaba
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.,Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| |
Collapse
|
16
|
Çoruh O, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Commun Biol 2021; 4:304. [PMID: 33686186 PMCID: PMC7940658 DOI: 10.1038/s42003-021-01808-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/05/2021] [Indexed: 01/31/2023] Open
Abstract
A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700.
Collapse
Affiliation(s)
- Orkun Çoruh
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Anna Frank
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany
| | - Hideaki Tanaka
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Akihiro Kawamoto
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Eithar El-Mohsnawy
- Department of Botany and Microbiology, Faculty of Science, Kafrelsheikh University, Kafr Al Sheikh, Egypt
| | - Takayuki Kato
- Laboratory of CryoEM Structural Biology, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- RIKEN Center for Biosystems Dynamics Research and SPring-8 Center, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
| | - Christoph Gerle
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
| | - Marc M Nowaczyk
- Plant Biochemistry, Faculty of Biology and Biotechnology, Ruhr-University Bochum, Bochum, Germany.
| | - Genji Kurisu
- Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
- Department of Macromolecular Science, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan.
| |
Collapse
|
17
|
OUP accepted manuscript. Microscopy (Oxf) 2021; 71:i3-i14. [DOI: 10.1093/jmicro/dfab049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/19/2021] [Accepted: 12/21/2021] [Indexed: 11/13/2022] Open
|
18
|
Naitow H, Hamaguchi T, Maki-Yonekura S, Isogai M, Yoshikawa N, Yonekura K. Apple latent spherical virus structure with stable capsid frame supports quasi-stable protrusions expediting genome release. Commun Biol 2020; 3:488. [PMID: 32887929 PMCID: PMC7474077 DOI: 10.1038/s42003-020-01217-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 08/11/2020] [Indexed: 01/30/2023] Open
Abstract
Picorna-like plant viruses are non-enveloped RNA spherical viruses of ~30 nm. Part of the survival of these viruses depends on their capsid being stable enough to harbour the viral genome and yet malleable enough to allow its release. However, molecular mechanisms remain obscure. Here, we report a structure of a picorna-like plant virus, apple latent spherical virus, at 2.87 Å resolution by single-particle cryo-electron microscopy (cryo-EM) with a cold-field emission beam. The cryo-EM map reveals a unique structure composed of three capsid proteins Vp25, Vp20, and Vp24. Strikingly Vp25 has a long N-terminal extension, which substantially stabilises the capsid frame of Vp25 and Vp20 subunits. Cryo-EM images also resolve RNA genome leaking from a pentameric protrusion of Vp24 subunits. The structures and observations suggest that genome release occurs through occasional opening of the Vp24 subunits, possibly suppressed to a low frequency by the rigid frame of the other subunits.
Collapse
Affiliation(s)
- Hisashi Naitow
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Saori Maki-Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Masamichi Isogai
- Plant Pathology Laboratory, Faculty of Agriculture, Iwate University, Ueda 3-chome 18-8, Morioka, Iwate, 020-8550, Japan
| | - Nobuyuki Yoshikawa
- Agri-Innovation Center, Iwate University, Ueda 3-chome 18-8, Morioka, Iwate, 020-8550, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan. .,Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
| |
Collapse
|
19
|
Shigematsu H. Electron cryo-microscopy for elucidating the dynamic nature of live-protein complexes. Biochim Biophys Acta Gen Subj 2020; 1864:129436. [DOI: 10.1016/j.bbagen.2019.129436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 08/31/2019] [Accepted: 09/11/2019] [Indexed: 12/30/2022]
|
20
|
Hamaguchi T, Maki-Yonekura S, Naitow H, Matsuura Y, Ishikawa T, Yonekura K. A new cryo-EM system for single particle analysis. J Struct Biol 2019; 207:40-48. [DOI: 10.1016/j.jsb.2019.04.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 03/16/2019] [Accepted: 04/13/2019] [Indexed: 11/29/2022]
|
21
|
Yonekura K, Ishikawa T, Maki-Yonekura S. A new cryo-EM system for electron 3D crystallography by eEFD. J Struct Biol 2019; 206:243-253. [PMID: 30928615 DOI: 10.1016/j.jsb.2019.03.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 03/13/2019] [Accepted: 03/26/2019] [Indexed: 10/27/2022]
Abstract
A new cryo-EM system has been developed and investigated for use in protein electron 3D crystallography. The system provides parallel illumination of a coherent 300 kV electron beam to a sample, filters out energy-loss electrons through the sample with an in-column energy filter, and allows rotational data collection on a fast camera. It also possesses motorized cryo-sample loading and automated liquid-nitrogen filling for cooling of multiple samples. To facilitate its use, we developed GUI programs for efficient operation and accurate structure analysis. Here we report on the performance of the system and first results for thin 3D crystals of the protein complexes, catalase and membrane protein complex ExbBD. Data quality is remarkably improved with this approach, which we name eEFD (electron energy-filtered diffraction of 3D crystals), compared with those collected at 200 kV without energy filtration. Key advances include precise control of the microscope and recordings of lens fluctuations, which the programs process and respond to. We also discuss the merits of higher-energy electrons and filtration of energy-loss electrons in electron 3D crystallography.
Collapse
Affiliation(s)
- Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN, SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.
| | | | - Saori Maki-Yonekura
- Biostructural Mechanism Laboratory, RIKEN, SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| |
Collapse
|
22
|
Natesh R. Single-Particle cryo-EM as a Pipeline for Obtaining Atomic Resolution Structures of Druggable Targets in Preclinical Structure-Based Drug Design. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2019. [PMCID: PMC7121590 DOI: 10.1007/978-3-030-05282-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-particle cryo-electron microscopy (cryo-EM) and three-dimensional (3D) image processing have gained importance in the last few years to obtain atomic structures of drug targets. Obtaining atomic-resolution 3D structure better than ~2.5 Å is a standard approach in pharma companies to design and optimize therapeutic compounds against drug targets like proteins. Protein crystallography is the main technique in solving the structures of drug targets at atomic resolution. However, this technique requires protein crystals which in turn is a major bottleneck. It was not possible to obtain the structure of proteins better than 2.5 Å resolution by any other methods apart from protein crystallography until 2015. Recent advances in single-particle cryo-EM and 3D image processing have led to a resolution revolution in the field of structural biology that has led to high-resolution protein structures, thus breaking the cryo-EM resolution barriers to facilitate drug discovery. There are 24 structures solved by single-particle cryo-EM with resolution 2.5 Å or better in the EMDataBank (EMDB) till date. Among these, five cryo-EM 3D reconstructions of proteins in the EMDB have their associated coordinates deposited in Protein Data Bank (PDB), with bound inhibitor/ ligand. Thus, for the first time, single-particle cryo-EM was included in the structure-based drug design (SBDD) pipeline for solving protein structures independently or where crystallography has failed to crystallize the protein. Further, this technique can be complementary and supplementary to protein crystallography field in solving 3D structures. Thus, single-particle cryo-EM can become a standard approach in pharmaceutical industry in the design, validation, and optimization of therapeutic compounds targeting therapeutically important protein molecules during preclinical drug discovery research. The present chapter will describe briefly the history and the principles of single-particle cryo-EM and 3D image processing to obtain atomic-resolution structure of proteins and their complex with their drug targets/ligands.
Collapse
|
23
|
Baldwin PR, Tan YZ, Eng ET, Rice WJ, Noble AJ, Negro CJ, Cianfrocco MA, Potter CS, Carragher B. Big data in cryoEM: automated collection, processing and accessibility of EM data. Curr Opin Microbiol 2017; 43:1-8. [PMID: 29100109 DOI: 10.1016/j.mib.2017.10.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/27/2017] [Accepted: 10/09/2017] [Indexed: 11/24/2022]
Abstract
The scope and complexity of cryogenic electron microscopy (cryoEM) data has greatly increased, and will continue to do so, due to recent and ongoing technical breakthroughs that have led to much improved resolutions for macromolecular structures solved using this method. This big data explosion includes single particle data as well as tomographic tilt series, both generally acquired as direct detector movies of ∼10-100 frames per image or per tilt-series. We provide a brief survey of the developments leading to the current status, and describe existing cryoEM pipelines, with an emphasis on the scope of data acquisition, methods for automation, and use of cloud storage and computing.
Collapse
Affiliation(s)
- Philip R Baldwin
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Yong Zi Tan
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Edward T Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - William J Rice
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Alex J Noble
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Carl J Negro
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Michael A Cianfrocco
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
24
|
Liu Z, Gutierrez-Vargas C, Wei J, Grassucci RA, Sun M, Espina N, Madison-Antenucci S, Tong L, Frank J. Determination of the ribosome structure to a resolution of 2.5 Å by single-particle cryo-EM. Protein Sci 2016; 26:82-92. [PMID: 27750394 DOI: 10.1002/pro.3068] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 11/06/2022]
Abstract
With the advance of new instruments and algorithms, and the accumulation of experience over decades, single-particle cryo-EM has become a pivotal part of structural biology. Recently, we determined the structure of a eukaryotic ribosome at 2.5 Å for the large subunit. The ribosome was derived from Trypanosoma cruzi, the protozoan pathogen of Chagas disease. The high-resolution density map allowed us to discern a large number of unprecedented details including rRNA modifications, water molecules, and ions such as Mg2+ and Zn2+ . In this paper, we focus on the procedures for data collection, image processing, and modeling, with particular emphasis on factors that contributed to the attainment of high resolution. The methods described here are readily applicable to other macromolecules for high-resolution reconstruction by single-particle cryo-EM.
Collapse
Affiliation(s)
- Zheng Liu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, 10032
| | - Cristina Gutierrez-Vargas
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York, 10032
| | - Jia Wei
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York, 10032
| | - Robert A Grassucci
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, 10032
| | - Ming Sun
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York, 10032
| | - Noel Espina
- Division of Infectious Diseases, New York State Department of Health, Wadsworth Center, Albany, New York, 12201
| | - Susan Madison-Antenucci
- Division of Infectious Diseases, New York State Department of Health, Wadsworth Center, Albany, New York, 12201
| | - Liang Tong
- Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York, 10032
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, 10032.,Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, New York, New York, 10032.,Department of Biological Sciences, Columbia University, New York, New York, 10027
| |
Collapse
|
25
|
Vargas J, Franken E, Sorzano COS, Gomez-Blanco J, Schoenmakers R, Koster AJ, Carazo JM. Foil-hole and data image quality assessment in 3DEM: Towards high-throughput image acquisition in the electron microscope. J Struct Biol 2016; 196:515-524. [PMID: 27725258 DOI: 10.1016/j.jsb.2016.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 10/06/2016] [Accepted: 10/06/2016] [Indexed: 11/19/2022]
Abstract
Automatic or semiautomatic data collection approaches on a transmission electron microscope (TEM) for Single Particle Analysis, capable of acquiring large datasets composed of only high quality images, are of great importance to obtain 3D density maps with the highest resolution possible. Typically, this task is performed by an experienced microscopist, who manually decides to keep or discard images according to subjective criteria. Therefore, this methodology is slow, intensive in human work and subjective. In this work, we propose a method to automatically or semiautomatically perform this image selection task. The approach is based on some simple, fast and effective image quality descriptors, which can be computed during acquisition, to characterize foil-hole and data images. The proposed approach has been used to evaluate the quality of different datasets consisting of foil-hole and data images obtained with a FEI Titan Krios electron microscope. The results show that the proposed method is very effective evaluating the quality of foil-hole and data images, as well as predicting the quality of the data images from the foil-hole images.
Collapse
Affiliation(s)
- J Vargas
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Cantoblanco (Madrid), Spain.
| | - E Franken
- FEI Company, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - C O S Sorzano
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Cantoblanco (Madrid), Spain
| | - J Gomez-Blanco
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Cantoblanco (Madrid), Spain
| | - R Schoenmakers
- FEI Company, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - A J Koster
- Koster Lab, Department of Molecular Cell Biology, Section Electron Microscopy, Leiden University Medical Center, Leiden, The Netherlands
| | - J M Carazo
- Biocomputing Unit, Centro Nacional de Biotecnología-CSIC, C/ Darwin 3, 28049 Cantoblanco (Madrid), Spain
| |
Collapse
|
26
|
Tan YZ, Cheng A, Potter CS, Carragher B. Automated data collection in single particle electron microscopy. Microscopy (Oxf) 2015; 65:43-56. [PMID: 26671944 DOI: 10.1093/jmicro/dfv369] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/06/2015] [Indexed: 11/12/2022] Open
Abstract
Automated data collection is an integral part of modern workflows in single particle electron microscopy (EM) research. This review surveys the software packages available for automated single particle EM data collection. The degree of automation at each stage of data collection is evaluated, and the capabilities of the software packages are described. Finally, future trends in automation are discussed.
Collapse
Affiliation(s)
- Yong Zi Tan
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Anchi Cheng
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, New York Structural Biology Center, New York, NY 10027, USA Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, NY 10027, USA Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| |
Collapse
|
27
|
Si D, He J. Tracing Beta Strands Using StrandTwister from Cryo-EM Density Maps at Medium Resolutions. Structure 2014; 22:1665-76. [DOI: 10.1016/j.str.2014.08.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 08/07/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
|
28
|
Costa A, Renault L, Swuec P, Petojevic T, Pesavento JJ, Ilves I, MacLellan-Gibson K, Fleck RA, Botchan MR, Berger JM. DNA binding polarity, dimerization, and ATPase ring remodeling in the CMG helicase of the eukaryotic replisome. eLife 2014; 3:e03273. [PMID: 25117490 PMCID: PMC4359367 DOI: 10.7554/elife.03273] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 08/08/2014] [Indexed: 01/29/2023] Open
Abstract
The Cdc45/Mcm2-7/GINS (CMG) helicase separates DNA strands during replication in eukaryotes. How the CMG is assembled and engages DNA substrates remains unclear. Using electron microscopy, we have determined the structure of the CMG in the presence of ATPγS and a DNA duplex bearing a 3' single-stranded tail. The structure shows that the MCM subunits of the CMG bind preferentially to single-stranded DNA, establishes the polarity by which DNA enters into the Mcm2-7 pore, and explains how Cdc45 helps prevent DNA from dissociating from the helicase. The Mcm2-7 subcomplex forms a cracked-ring, right-handed spiral when DNA and nucleotide are bound, revealing unexpected congruencies between the CMG and both bacterial DnaB helicases and the AAA+ motor of the eukaryotic proteasome. The existence of a subpopulation of dimeric CMGs establishes the subunit register of Mcm2-7 double hexamers and together with the spiral form highlights how Mcm2-7 transitions through different conformational and assembly states as it matures into a functional helicase.
Collapse
Affiliation(s)
- Alessandro Costa
- London Research Institute, Cancer Research UK, London, United Kingdom
| | - Ludovic Renault
- London Research Institute, Cancer Research UK, London, United Kingdom Department of Imaging, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Paolo Swuec
- London Research Institute, Cancer Research UK, London, United Kingdom
| | - Tatjana Petojevic
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - James J Pesavento
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Ivar Ilves
- Institute of Technology, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Kirsty MacLellan-Gibson
- Department of Imaging, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Roland A Fleck
- Department of Imaging, National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Michael R Botchan
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, United States
| |
Collapse
|
29
|
Penczek PA, Fang J, Li X, Cheng Y, Loerke J, Spahn CMT. CTER-rapid estimation of CTF parameters with error assessment. Ultramicroscopy 2014; 140:9-19. [PMID: 24562077 DOI: 10.1016/j.ultramic.2014.01.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 01/22/2014] [Accepted: 01/27/2014] [Indexed: 10/25/2022]
Abstract
In structural electron microscopy, the accurate estimation of the Contrast Transfer Function (CTF) parameters, particularly defocus and astigmatism, is of utmost importance for both initial evaluation of micrograph quality and for subsequent structure determination. Due to increases in the rate of data collection on modern microscopes equipped with new generation cameras, it is also important that the CTF estimation can be done rapidly and with minimal user intervention. Finally, in order to minimize the necessity for manual screening of the micrographs by a user it is necessary to provide an assessment of the errors of fitted parameters values. In this work we introduce CTER, a CTF parameters estimation method distinguished by its computational efficiency. The efficiency of the method makes it suitable for high-throughput EM data collection, and enables the use of a statistical resampling technique, bootstrap, that yields standard deviations of estimated defocus and astigmatism amplitude and angle, thus facilitating the automation of the process of screening out inferior micrograph data. Furthermore, CTER also outputs the spatial frequency limit imposed by reciprocal space aliasing of the discrete form of the CTF and the finite window size. We demonstrate the efficiency and accuracy of CTER using a data set collected on a 300kV Tecnai Polara (FEI) using the K2 Summit DED camera in super-resolution counting mode. Using CTER we obtained a structure of the 80S ribosome whose large subunit had a resolution of 4.03Å without, and 3.85Å with, inclusion of astigmatism parameters.
Collapse
Affiliation(s)
- Pawel A Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, 6431 Fannin MSB 6.220, Houston, TX 77054, USA.
| | - Jia Fang
- Department of Biochemistry and Molecular Biology, The University of Texas Medical School, 6431 Fannin MSB 6.220, Houston, TX 77054, USA
| | - Xueming Li
- The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Yifan Cheng
- The Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Justus Loerke
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| |
Collapse
|
30
|
Rochat RH, Hecksel CW, Chiu W. Cryo-EM techniques to resolve the structure of HSV-1 capsid-associated components. Methods Mol Biol 2014; 1144:265-81. [PMID: 24671690 DOI: 10.1007/978-1-4939-0428-0_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Electron cryo-microscopy has become a routine technique to determine the structure of biochemically purified herpes simplex virus capsid particles. This chapter describes the procedures of specimen preparation by cryopreservation; low dose and low temperature imaging in an electron cryo-microscope; and data processing for reconstruction. This methodology has yielded subnanometer resolution structures of the icosahedral capsid shell where α-helices and β-sheets of individual subunits can be recognized. A relaxation of the symmetry in the reconstruction steps allows us to resolve the DNA packaging protein located at one of the 12 vertices in the capsid.
Collapse
Affiliation(s)
- Ryan H Rochat
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | | |
Collapse
|
31
|
Guichard JA, Middleton PC, McConnell MR. Genetic analysis of structural proteins in the adsorption apparatus of bacteriophage epsilon 15. World J Virol 2013; 2:152-159. [PMID: 24286036 PMCID: PMC3832910 DOI: 10.5501/wjv.v2.i4.152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/22/2013] [Accepted: 10/16/2013] [Indexed: 02/05/2023] Open
Abstract
AIM: To probe the organizational structure of the adsorption apparatus of bacteriophage epsilon 15 (E15) using genetic and biochemical methodology
METHODS: Hydroxylamine was used to create nonsense mutants of bacteriophage E15. The mutants were then screened for defects in their adsorption apparatus proteins, initially by measuring the concentrations of free tail spike proteins in lysates of cells that had been infected by the phage mutants under non-permissive growth conditions. Phage strains whose infected cell lysates contained above-average levels of free tail spike protein under non-permissive growth conditions were assumed to contain nonsense mutations in genes coding for adsorption apparatus proteins. These mutants were characterized by classical genetic mapping methods as well as automated sequencing of several of their genes. Finally, sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography were used to examine the protein compositions of the radioactive particles produced when the various mutants were grown on a non-permissive host cell in the presence of 35S-methionine and co-purified along with E15wt phage on CsCl block gradients.
RESULTS: Our results are consistent with gp4 forming the portal ring structure of E15. In addition, they show that proteins gp15 and gp17 likely comprise the central tube portion of the E15 adsorption apparatus, with gp17 being more distally positioned than gp15 and dependent upon both gp15 and gp16 for its attachment. Finally, our data indicates that tail spike proteins comprised of gp20 can assemble onto nascent virions that contain gp7, gp10, gp4 and packaged DNA, but which lack both gp15 and gp17, thereby forming particles that are of sufficient stability to survive CsCl buoyant density centrifugation.
CONCLUSION: The portal ring (gp4) of E15 is bound to tail spikes (gp20) and the tail tube (gp15 and gp17); gp17’s attachment requires both gp15 and gp16.
Collapse
|
32
|
Abstract
Single particle electron microscopy is a versatile technique for the structural analysis of protein complexes in near-native conditions. While tremendous progress has been made during the past few decades in techniques for specimen preparation, imaging, and image analysis, the field is still in development. In the context of this volume on electron crystallography, the following chapter gives practical guidelines on how to begin single particle EM studies, including preparing specimens, selecting imaging conditions, and choosing which of the many approaches to image analysis are appropriate for a specific sample.
Collapse
Affiliation(s)
- Wilson C Y Lau
- Molecular Structure and Function Program, Departments of Biochemistry and Medical Biophysics, The Hospital for Sick Children, The University of Toronto, Toronto, ON, Canada
| | | |
Collapse
|
33
|
Rees I, Langley E, Chiu W, Ludtke SJ. EMEN2: an object oriented database and electronic lab notebook. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2013; 19:1-10. [PMID: 23360752 PMCID: PMC3907281 DOI: 10.1017/s1431927612014043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Transmission electron microscopy and associated methods, such as single particle analysis, two-dimensional crystallography, helical reconstruction, and tomography, are highly data-intensive experimental sciences, which also have substantial variability in experimental technique. Object-oriented databases present an attractive alternative to traditional relational databases for situations where the experiments themselves are continually evolving. We present EMEN2, an easy to use object-oriented database with a highly flexible infrastructure originally targeted for transmission electron microscopy and tomography, which has been extended to be adaptable for use in virtually any experimental science. It is a pure object-oriented database designed for easy adoption in diverse laboratory environments and does not require professional database administration. It includes a full featured, dynamic web interface in addition to APIs for programmatic access. EMEN2 installations currently support roughly 800 scientists worldwide with over 1/2 million experimental records and over 20 TB of experimental data. The software is freely available with complete source.
Collapse
Affiliation(s)
- Ian Rees
- Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030
| | - Ed Langley
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Wah Chiu
- Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| | - Steven J. Ludtke
- Graduate Program of Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030
- Verna and Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 77030
| |
Collapse
|
34
|
Abstract
Membrane proteins play a tremendously important role in cell physiology and serve as a target for an increasing number of drugs. Structural information is key to understanding their function and for developing new strategies for combating disease. However, the complex physical chemistry associated with membrane proteins has made them more difficult to study than their soluble cousins. Electron crystallography has historically been a successful method for solving membrane protein structures and has the advantage of providing a native lipid environment for these proteins. Specifically, when membrane proteins form two-dimensional arrays within a lipid bilayer, electron microscopy can be used to collect images and diffraction and the corresponding data can be combined to produce a three-dimensional reconstruction, which under favorable conditions can extend to atomic resolution. Like X-ray crystallography, the quality of the structures are very much dependent on the order and size of the crystals. However, unlike X-ray crystallography, high-throughput methods for screening crystallization trials for electron crystallography are not in general use. In this chapter, we describe two alternative methods for high-throughput screening of membrane protein crystallization within the lipid bilayer. The first method relies on the conventional use of dialysis for removing detergent and thus reconstituting the bilayer; an array of dialysis wells in the standard 96-well format allows the use of a liquid-handling robot and greatly increases throughput. The second method relies on titration of cyclodextrin as a chelating agent for detergent; a specialized pipetting robot has been designed not only to add cyclodextrin in a systematic way, but to use light scattering to monitor the reconstitution process. In addition, the use of liquid-handling robots for making negatively stained grids and methods for automatically imaging samples in the electron microscope are described.
Collapse
|
35
|
Abstract
General considerations for using automation software for acquiring high-resolution images of 2D crystals under low-dose conditions are presented. Protocol modifications specific to this application in Leginon are provided.
Collapse
Affiliation(s)
- Anchi Cheng
- Department of Cell Biology, The National Resource for Automated Molecular Microscopy, The Scripps Research Institute, La Jolla, CA, USA
| |
Collapse
|
36
|
Burger V, Chennubhotla C. Nhs: network-based hierarchical segmentation for cryo-electron microscopy density maps. Biopolymers 2012; 97:732-41. [PMID: 22696408 PMCID: PMC3483038 DOI: 10.1002/bip.22041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cryo-electron microscopy (cryo-EM) experiments yield low-resolution (3-30 Å) 3D-density maps of macromolecules. These density maps are segmented to identify structurally distinct proteins, protein domains, and subunits. Such partitioning aids the inference of protein motions and guides fitting of high-resolution atomistic structures. Cryo-EM density map segmentation has traditionally required tedious and subjective manual partitioning or semisupervised computational methods, whereas validation of resulting segmentations has remained an open problem in this field. We introduce a network-based hierarchical segmentation (Nhs) method, that provides a multi-scale partitioning, reflecting local and global clustering, while requiring no user input. This approach models each map as a graph, where map voxels constitute nodes and weighted edges connect neighboring voxels. Nhs initiates Markov diffusion (or random walk) on the weighted graph. As Markov probabilities homogenize through diffusion, an intrinsic segmentation emerges. We validate the segmentations with ground-truth maps based on atomistic models. When implemented on density maps in the 2010 Cryo-EM Modeling Challenge, Nhs efficiently and objectively partitions macromolecules into structurally and functionally relevant subregions at multiple scales.
Collapse
Affiliation(s)
- Virginia Burger
- Joint CMU-Pitt Ph.D. Program in Computational Biology, University of Pittsburgh School of Medicine
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine
| | - Chakra Chennubhotla
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine
| |
Collapse
|
37
|
Baker ML, Baker MR, Hryc CF, Ju T, Chiu W. Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps. Biopolymers 2012; 97:655-68. [PMID: 22696403 PMCID: PMC3899894 DOI: 10.1002/bip.22065] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The complex interplay of proteins and other molecules, often in the form of large transitory assemblies, are critical to cellular function. Today, X-ray crystallography and electron cryo-microscopy (cryo-EM) are routinely used to image these macromolecular complexes, though often at limited resolutions. Despite the rapidly growing number of macromolecular structures, few tools exist for modeling and annotating structures in the range of 3-10 Å resolution. To address this need, we have developed a number of utilities specifically targeting subnanometer resolution density maps. As part of the 2010 Cryo-EM Modeling Challenge, we demonstrated two of our latest de novo modeling tools, Pathwalking and Gorgon, as well as a tool for secondary structure identification (SSEHunter) and a new rigid-body/flexible fitting tool in Gorgon. In total, we submitted 30 structural models from ten different subnanometer resolution data sets in four of the six challenge categories. Each of our utlities produced accurate structural models and annotations across the various density maps. In the end, the utilities that we present here offer users a robust toolkit for analyzing and modeling protein structure in macromolecular assemblies at non-atomic resolutions.
Collapse
Affiliation(s)
- Matthew L Baker
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, Houston, TX 77030, USA.
| | | | | | | | | |
Collapse
|
38
|
Zhang Q, Bettadapura R, Bajaj C. Macromolecular structure modeling from 3D EM using VolRover 2.0. Biopolymers 2012; 97:709-31. [PMID: 22696407 DOI: 10.1002/bip.22052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We review tools for structure identification and model-based refinement from three-dimensional electron microscopy implemented in our in-house software package, VOLROVER 2.0. For viral density maps with icosahedral symmetry, we segment the capsid, polymeric, and monomeric subunits using techniques based on automatic symmetry detection and multidomain fast marching. For large biomolecules without symmetry information, we again use our multidomain fast-marching method with manual or fit-based multiseeding to segment meaningful substructures. In either case, we subject the resulting segmented subunit to secondary structure detection when the EM resolution is sufficiently high, and rigid-body structure fitting when the corresponding X-ray structure is available. Secondary structure elements are identified by three techniques: our earlier volume-based and boundary-based skeletonization methods as well as a new method, currently in development, based on solving the grassfire flow equation. For rigid-body fitting, we adapt our earlier fast Fourier-based correlation scheme F2Dock. Our reported segmentation, secondary structure elements identification, and rigid-body fitting techniques, implemented in VOLROVER 2.0 are applied to the PSB 2011 cryo-EM modeling challenge data, and our results are briefly compared to similar results submitted from other research groups. The comparisons show that our techniques are equally capable of segmenting relatively accurate subunits from a viral or protein assembly, and that high segmentation quality leads in turn to higher-quality results of secondary structure elements identification and correlation-based rigid-body fitting. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 709-731, 2012.
Collapse
Affiliation(s)
- Qin Zhang
- Institute for Computational Engineering and Sciences, The University of Texas, Austin, TX 78712, USA
| | | | | |
Collapse
|
39
|
Penczek PA, Kimmel M, Spahn CMT. Identifying conformational states of macromolecules by eigen-analysis of resampled cryo-EM images. Structure 2012; 19:1582-90. [PMID: 22078558 DOI: 10.1016/j.str.2011.10.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 09/20/2011] [Accepted: 10/06/2011] [Indexed: 11/16/2022]
Abstract
We present the codimensional principal component analysis (PCA), a novel and straightforward method for resolving sample heterogeneity within a set of cryo-EM 2D projection images of macromolecular assemblies. The method employs PCA of resampled 3D structures computed using subsets of 2D data obtained with a novel hypergeometric sampling scheme. PCA provides us with a small subset of dominating "eigenvolumes" of the system, whose reprojections are compared with experimental projection data to yield their factorial coordinates constructed in a common framework of the 3D space of the macromolecule. Codimensional PCA is unique in the dramatic reduction of dimensionality of the problem, which facilitates rapid determination of both the plausible number of conformers in the sample and their 3D structures. We applied the codimensional PCA to a complex data set of Thermus thermophilus 70S ribosome, and we identified four major conformational states and visualized high mobility of the stalk base region.
Collapse
Affiliation(s)
- Pawel A Penczek
- Department of Biochemistry and Molecular Biology, Houston Medical School, The University of Texas, Houston, TX 77030, USA.
| | | | | |
Collapse
|
40
|
Bammes BE, Rochat RH, Jakana J, Chen DH, Chiu W. Direct electron detection yields cryo-EM reconstructions at resolutions beyond 3/4 Nyquist frequency. J Struct Biol 2012; 177:589-601. [PMID: 22285189 DOI: 10.1016/j.jsb.2012.01.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 12/21/2011] [Accepted: 01/11/2012] [Indexed: 11/28/2022]
Abstract
One limitation in electron cryo-microscopy (cryo-EM) is the inability to recover high-resolution signal from the image-recording media at the full-resolution limit of the transmission electron microscope. Direct electron detection using CMOS-based sensors for digitally recording images has the potential to alleviate this shortcoming. Here, we report a practical performance evaluation of a Direct Detection Device (DDD®) for biological cryo-EM at two different microscope voltages: 200 and 300 kV. Our DDD images of amorphous and graphitized carbon show strong per-pixel contrast with image resolution near the theoretical sampling limit of the data. Single-particle reconstructions of two frozen-hydrated bacteriophages, P22 and ε15, establish that the DDD is capable of recording usable signal for 3D reconstructions at about 4/5 of the Nyquist frequency, which is a vast improvement over the performance of conventional imaging media. We anticipate the unparalleled performance of this digital recording device will dramatically benefit cryo-EM for routine tomographic and single-particle structural determination of biological specimens.
Collapse
Affiliation(s)
- Benjamin E Bammes
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | |
Collapse
|
41
|
Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 726:49-90. [PMID: 22297510 DOI: 10.1007/978-1-4614-0980-9_4] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The past few decades have seen tremendous advances in single-particle electron -cryo-microscopy (cryo-EM). The field has matured to the point that near-atomic resolution density maps can be generated for icosahedral viruses without the need for crystallization. In parallel, substantial progress has been made in determining the structures of nonicosahedrally arranged proteins in viruses by employing either single-particle cryo-EM or cryo-electron tomography (cryo-ET). Implicit in this course have been the availability of a new generation of electron cryo-microscopes and the development of the computational tools that are essential for generating these maps and models. This methodology has enabled structural biologists to analyze structures in increasing detail for virus particles that are in different morphogenetic states. Furthermore, electron imaging of frozen, hydrated cells, in the process of being infected by viruses, has also opened up a new avenue for studying virus structures "in situ". Here we present the common techniques used to acquire and process cryo-EM and cryo-ET data and discuss their implications for structural virology both now and in the future.
Collapse
|
42
|
Orlova EV, Saibil HR. Structural analysis of macromolecular assemblies by electron microscopy. Chem Rev 2011; 111:7710-48. [PMID: 21919528 PMCID: PMC3239172 DOI: 10.1021/cr100353t] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Indexed: 12/11/2022]
Affiliation(s)
- E. V. Orlova
- Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
| | - H. R. Saibil
- Crystallography and Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, United Kingdom
| |
Collapse
|
43
|
Kylberg G, Uppström M, Hedlund KO, Borgefors G, Sintorn IM. Segmentation of virus particle candidates in transmission electron microscopy images. J Microsc 2011; 245:140-7. [PMID: 21972793 DOI: 10.1111/j.1365-2818.2011.03556.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper, we present an automatic segmentation method that detects virus particles of various shapes in transmission electron microscopy images. The method is based on a statistical analysis of local neighbourhoods of all the pixels in the image followed by an object width discrimination and finally, for elongated objects, a border refinement step. It requires only one input parameter, the approximate width of the virus particles searched for. The proposed method is evaluated on a large number of viruses. It successfully segments viruses regardless of shape, from polyhedral to highly pleomorphic.
Collapse
Affiliation(s)
- G Kylberg
- Centre for Image Analysis, Swedish University of Agricultural Sciences and Uppsala University, Uppsala, Sweden.
| | | | | | | | | |
Collapse
|
44
|
Korinek A, Beck F, Baumeister W, Nickell S, Plitzko JM. Computer controlled cryo-electron microscopy – TOM2 a software package for high-throughput applications. J Struct Biol 2011; 175:394-405. [DOI: 10.1016/j.jsb.2011.06.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 06/02/2011] [Accepted: 06/06/2011] [Indexed: 12/01/2022]
|
45
|
Bammes BE, Rochat RH, Jakana J, Chiu W. Practical performance evaluation of a 10k × 10k CCD for electron cryo-microscopy. J Struct Biol 2011; 175:384-93. [PMID: 21619932 DOI: 10.1016/j.jsb.2011.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Revised: 05/09/2011] [Accepted: 05/10/2011] [Indexed: 11/18/2022]
Abstract
Electron cryo-microscopy (cryo-EM) images are commonly collected using either charge-coupled devices (CCD) or photographic film. Both film and the current generation of 16 megapixel (4k × 4k) CCD cameras have yielded high-resolution structures. Yet, despite the many advantages of CCD cameras, more than two times as many structures of biological macromolecules have been published in recent years using photographic film. The continued preference to film, especially for subnanometer-resolution structures, may be partially influenced by the finer sampling and larger effective specimen imaging area offered by film. Large format digital cameras may finally allow them to overtake film as the preferred detector for cryo-EM. We have evaluated a 111-megapixel (10k × 10k) CCD camera with a 9 μm pixel size. The spectral signal-to-noise ratios of low dose images of carbon film indicate that this detector is capable of providing signal up to at least 2/5 Nyquist frequency potentially retrievable for 3D reconstructions of biological specimens, resulting in more than double the effective specimen imaging area of existing 4k × 4k CCD cameras. We verified our estimates using frozen-hydrated ε15 bacteriophage as a biological test specimen with previously determined structure, yielding a ∼7 Å resolution single particle reconstruction from only 80 CCD frames. Finally, we explored the limits of current CCD technology by comparing the performance of this detector to various CCD cameras used for recording data yielding subnanometer resolution cryo-EM structures submitted to the electron microscopy data bank (http://www.emdatabank.org/).
Collapse
Affiliation(s)
- Benjamin E Bammes
- Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | |
Collapse
|
46
|
Marko M, Leith A, Hsieh C, Danev R. Retrofit implementation of Zernike phase plate imaging for cryo-TEM. J Struct Biol 2011; 174:400-12. [PMID: 21272647 DOI: 10.1016/j.jsb.2011.01.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 01/17/2011] [Accepted: 01/19/2011] [Indexed: 10/18/2022]
Abstract
In-focus phase-plate imaging is particularly beneficial for cryo-TEM because it offers a substantial overall increase in image contrast, without an electron dose penalty, and it simplifies image interpretation. We show how phase-plate cryo-TEM can be implemented with an appropriate existing TEM, and provide a basic practical introduction to use of thin-film (carbon) phase plates. We point out potential pitfalls of phase-plate operation, and discuss solutions. We provide information on evaluating a particular TEM for its suitability.
Collapse
Affiliation(s)
- Michael Marko
- Resource for Visualization of Biological Complexity, Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY 12201-0509, USA.
| | | | | | | |
Collapse
|
47
|
Saha M, Levitt M, Chiu W. MOTIF-EM: an automated computational tool for identifying conserved regions in CryoEM structures. Bioinformatics 2010; 26:i301-9. [PMID: 20529921 PMCID: PMC2881380 DOI: 10.1093/bioinformatics/btq195] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We present a new, first-of-its-kind, fully automated computational tool MOTIF-EM for identifying regions or domains or motifs in cryoEM maps of large macromolecular assemblies (such as chaperonins, viruses, etc.) that remain conformationally conserved. As a by-product, regions in structures that are not conserved are revealed: this can indicate local molecular flexibility related to biological activity. MOTIF-EM takes cryoEM volumetric maps as inputs. The technique used by MOTIF-EM to detect conserved sub-structures is inspired by a recent breakthrough in 2D object recognition. The technique works by constructing rotationally invariant, low-dimensional representations of local regions in the input cryoEM maps. Correspondences are established between the reduced representations (by comparing them using a simple metric) across the input maps. The correspondences are clustered using hash tables and graph theory is used to retrieve conserved structural domains or motifs. MOTIF-EM has been used to extract conserved domains occurring in large macromolecular assembly maps, including as those of viruses P22 and epsilon 15, Ribosome 70S, GroEL, that remain structurally conserved in different functional states. Our method can also been used to build atomic models for some maps. We also used MOTIF-EM to identify the conserved folds shared among dsDNA bacteriophages HK97, Epsilon 15, and ô29, though they have low-sequence similarity. Contact:mitul@cs.stanford.edu Supplementary information:Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Mitul Saha
- NIH Center for Biomedical Computation, Stanford University, Stanford, CA 94305, USA.
| | | | | |
Collapse
|
48
|
Mitsuoka K. Obtaining high-resolution images of biological macromolecules by using a cryo-electron microscope with a liquid-helium cooled stage. Micron 2010; 42:100-6. [PMID: 20869255 DOI: 10.1016/j.micron.2010.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 08/20/2010] [Accepted: 08/21/2010] [Indexed: 10/19/2022]
Abstract
To obtain high-resolution images of biological macromolecules, a cryo-electron microscope (cryo-EM) is useful to preserve the hydrated state of the molecules. In addition, the cryo-conditions reduce some of the electron radiation damage, although averaging is necessary to obtain the molecular resolution from biological macromolecules. For the averaging, the three reconstruction methods of electron crystallography, helical reconstruction, and single particle analysis facilitate the determination of the atomic models. Here we describe suitable techniques for high-resolution imaging in these three different methods, based on our experiences using cryo-EM with a liquid-helium cooled stage. Irradiation damage by the electron beam is the most serious problem in the structural analysis of a biological specimen, and we clearly show that further reduction of the specimen temperature, from liquid nitrogen to liquid helium temperature, improves the cryo-protection factor by at least two-fold for both glucose-embedded and frozen-hydrated specimens. We review the image processing, and then discuss the future prospects of cryo-EM.
Collapse
Affiliation(s)
- Kaoru Mitsuoka
- National Institute of Advanced Industrial Science and Technology, Biomedicinal Information Research Center, 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan.
| |
Collapse
|
49
|
Nicholson WV, White H, Trinick J. An approach to automated acquisition of cryoEM images from lacey carbon grids. J Struct Biol 2010; 172:395-9. [PMID: 20817100 DOI: 10.1016/j.jsb.2010.08.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 08/22/2010] [Accepted: 08/29/2010] [Indexed: 10/19/2022]
Abstract
An approach to automated acquisition of cryoEM image data from lacey carbon grids using the Leginon program is described. Automated liquid nitrogen top up of the specimen holder dewar was used as a step towards full automation, without operator intervention during the course of data collection. During cryoEM studies of actin labelled with myosin V, we have found it necessary to work with lacey grids rather than Quantifoil or C-flat grids due to interaction of myosin V with the support film. Lacey grids have irregular holes of variable shape and size, in contrast to Quantifoil or C-flat grids which have a regular array of similar circular holes on each grid square. Other laboratories also prefer to work with grids with irregular holes for a variety of reasons. Therefore, it was necessary to develop a different strategy from normal Leginon usage for working with lacey grids for targeting holes for image acquisition and suitable areas for focussing prior to image acquisition. This approach was implemented by using the extensible framework provided by Leginon and by developing a new MSI application within that framework which includes a new Leginon node (for a novel method for finding focus targets).
Collapse
Affiliation(s)
- William V Nicholson
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, UK.
| | | | | |
Collapse
|
50
|
Clare DK, Orlova EV. 4.6A Cryo-EM reconstruction of tobacco mosaic virus from images recorded at 300 keV on a 4k x 4k CCD camera. J Struct Biol 2010; 171:303-8. [PMID: 20558300 PMCID: PMC2939825 DOI: 10.1016/j.jsb.2010.06.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 05/14/2010] [Accepted: 06/08/2010] [Indexed: 11/19/2022]
Abstract
Tobacco mosaic virus (TMV) is a plant virus with a highly ordered organisation and has been described in three different structural states: As stacked disks without RNA (X-ray crystallography), as a helical form with RNA (X-ray fibre diffraction) and as a second distinct helical form with RNA (cryo-EM). Here we present a structural analysis of TMV as a test object to assess the quality of cryo-EM images recorded at 300 keV on a CCD camera. The 4.6 Å TMV structure obtained is consistent with the previous cryo-EM structure and confirms that there is a second helical form of TMV. The structure here also shows that with a similar number of TMV segments an equivalent resolution can be achieved with a 4k CCD camera at 300 keV.
Collapse
|