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Horstmann A, Riggs S, Chaban Y, Clare DK, de Freitas G, Farmer D, Howe A, Morris KL, Hatton D. A service-based approach to cryoEM facility processing pipelines at eBIC. Acta Crystallogr D Struct Biol 2024; 80:174-180. [PMID: 38376453 PMCID: PMC10910546 DOI: 10.1107/s2059798324000986] [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] [Accepted: 01/29/2024] [Indexed: 02/21/2024] Open
Abstract
Electron cryo-microscopy image-processing workflows are typically composed of elements that may, broadly speaking, be categorized as high-throughput workloads which transition to high-performance workloads as preprocessed data are aggregated. The high-throughput elements are of particular importance in the context of live processing, where an optimal response is highly coupled to the temporal profile of the data collection. In other words, each movie should be processed as quickly as possible at the earliest opportunity. The high level of disconnected parallelization in the high-throughput problem directly allows a completely scalable solution across a distributed computer system, with the only technical obstacle being an efficient and reliable implementation. The cloud computing frameworks primarily developed for the deployment of high-availability web applications provide an environment with a number of appealing features for such high-throughput processing tasks. Here, an implementation of an early-stage processing pipeline for electron cryotomography experiments using a service-based architecture deployed on a Kubernetes cluster is discussed in order to demonstrate the benefits of this approach and how it may be extended to scenarios of considerably increased complexity.
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Affiliation(s)
- Anna Horstmann
- Data Analysis, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Stephen Riggs
- Data Analysis, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Yuriy Chaban
- Electron Bio-Imaging Centre (eBIC), Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Daniel K. Clare
- Electron Bio-Imaging Centre (eBIC), Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Guilherme de Freitas
- Scientific Information Management Systems, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - David Farmer
- Electron Bio-Imaging Centre (eBIC), Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Andrew Howe
- Electron Bio-Imaging Centre (eBIC), Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- Dubochet Centre for Imaging, University of Geneva, Quai Ernest-Ansermet 30, Geneva, Switzerland
| | - Kyle L. Morris
- Electron Bio-Imaging Centre (eBIC), Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
- EMDB (Electron Microscopy Data Bank), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Daniel Hatton
- Data Analysis, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
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2
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de la Cruz MJ, Eng ET. Scaling up cryo-EM for biology and chemistry: The journey from niche technology to mainstream method. Structure 2023; 31:1487-1498. [PMID: 37820731 PMCID: PMC10841453 DOI: 10.1016/j.str.2023.09.009] [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: 07/29/2023] [Revised: 08/31/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
Cryoelectron microscopy (cryo-EM) methods have made meaningful contributions in a wide variety of scientific research fields. In structural biology, cryo-EM routinely elucidates molecular structure from isolated biological macromolecular complexes or in a cellular context by harnessing the high-resolution power of the electron in order to image samples in a frozen, hydrated environment. For structural chemistry, the cryo-EM method popularly known as microcrystal electron diffraction (MicroED) has facilitated atomic structure generation of peptides and small molecules from their three-dimensional crystal forms. As cryo-EM has grown from an emerging technology, it has undergone modernization to enable multimodal transmission electron microscopy (TEM) techniques becoming more routine, reproducible, and accessible to accelerate research across multiple disciplines. We review recent advances in modern cryo-EM and assess how they are contributing to the future of the field with an eye to the past.
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Affiliation(s)
- M Jason de la Cruz
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Edward T Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA.
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3
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Patel KD, MacDonald MR, Ahmed SF, Singh J, Gulick AM. Structural advances toward understanding the catalytic activity and conformational dynamics of modular nonribosomal peptide synthetases. Nat Prod Rep 2023; 40:1550-1582. [PMID: 37114973 PMCID: PMC10510592 DOI: 10.1039/d3np00003f] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Indexed: 04/29/2023]
Abstract
Covering: up to fall 2022.Nonribosomal peptide synthetases (NRPSs) are a family of modular, multidomain enzymes that catalyze the biosynthesis of important peptide natural products, including antibiotics, siderophores, and molecules with other biological activity. The NRPS architecture involves an assembly line strategy that tethers amino acid building blocks and the growing peptides to integrated carrier protein domains that migrate between different catalytic domains for peptide bond formation and other chemical modifications. Examination of the structures of individual domains and larger multidomain proteins has identified conserved conformational states within a single module that are adopted by NRPS modules to carry out a coordinated biosynthetic strategy that is shared by diverse systems. In contrast, interactions between modules are much more dynamic and do not yet suggest conserved conformational states between modules. Here we describe the structures of NRPS protein domains and modules and discuss the implications for future natural product discovery.
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Affiliation(s)
- Ketan D Patel
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Monica R MacDonald
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Syed Fardin Ahmed
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Jitendra Singh
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
| | - Andrew M Gulick
- University at Buffalo, Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, 55 Main St. Buffalo, NY 14203, USA.
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4
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Sheng Y, Harrison PJ, Vogirala V, Yang Z, Strain-Damerell C, Frosio T, Himes BA, Siebert CA, Zhang P, Clare DK. Application of super-resolution and correlative double sampling in cryo-electron microscopy. Faraday Discuss 2022; 240:261-276. [PMID: 35938521 PMCID: PMC9642007 DOI: 10.1039/d2fd00049k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/24/2022] [Indexed: 01/09/2023]
Abstract
Developments in cryo-EM have allowed atomic or near-atomic resolution structure determination to become routine in single particle analysis (SPA). However, near-atomic resolution structures determined using cryo-electron tomography and sub-tomogram averaging (cryo-ET STA) are much less routine. In this paper, we show that collecting cryo-ET STA data using the same conditions as SPA, with both correlated double sampling (CDS) and the super-resolution mode, allowed apoferritin to be reconstructed out to the physical Nyquist frequency of the images. Even with just two tilt series, STA yields an apoferritin map at 2.9 Å resolution. These results highlight the exciting potential of cryo-ET STA in the future of protein structure determination. While processing SPA data recorded in super-resolution mode may yield structures surpassing the physical Nyquist limit, processing cryo-ET STA data in the super-resolution mode gave no additional resolution benefit. We further show that collecting SPA data in the super-resolution mode, with CDS activated, reduces the estimated B-factor, leading to a reduction in the number of particles required to reach a target resolution without compromising the data size on disk and the area imaged in SerialEM. However, collecting SPA data in CDS does reduce throughput, given that a similar resolution structure, with a slightly larger B-factor, is achievable with optimised parameters for speed in EPU (without CDS).
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Affiliation(s)
- Yuewen Sheng
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Peter J Harrison
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Vinod Vogirala
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Zhengyi Yang
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Claire Strain-Damerell
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
- RCaH, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Thomas Frosio
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Benjamin A Himes
- Howard Hughes Medical Institute, RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, USA
| | - C Alistair Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
| | - Peijun Zhang
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
- RCaH, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Daniel K Clare
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
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5
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Kelly J, Male A, Rubies N, Mahoney D, Walker JM, Gomez-Gonzalez MA, Wilkin G, Parker JE, Quinn PD. The Delta Robot-A long travel nano-positioning stage for scanning x-ray microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2022; 93:043712. [PMID: 35489936 DOI: 10.1063/5.0084806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
A new stage design concept, the Delta Robot, is presented, which is a parallel kinematic design for scanning x-ray microscopy applications. The stage employs three orthogonal voice coils, which actuate parallelogram flexures. The design has a 3 mm travel range and achieves rms position jitter, integrated from 1 Hz to 1 kHz, of 2.8 and 1.3 nm perpendicular to the beam and 5.6 nm along the beam direction with loads up to 350 g. The Delta Robot design process used a mechatronics approach of iterative modeling and simulation to develop the system and validate performance. The design considerations, design process, stability, and operational performance on the hard x-ray nanoprobe at Diamond Light Source are presented.
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Affiliation(s)
- Jon Kelly
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Andrew Male
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Nicholas Rubies
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - David Mahoney
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Jessica M Walker
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Miguel A Gomez-Gonzalez
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Guy Wilkin
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Julia E Parker
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Paul D Quinn
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
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6
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Zimanyi CM, Kopylov M, Potter CS, Carragher B, Eng ET. Broadening access to cryoEM through centralized facilities. Trends Biochem Sci 2022; 47:106-116. [PMID: 34823974 PMCID: PMC8760164 DOI: 10.1016/j.tibs.2021.10.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 02/03/2023]
Abstract
Cryogenic electron microscopy (cryoEM) uses images of frozen hydrated biological specimens to produce macromolecular structures, opening up previously inaccessible levels of biological organization to high-resolution structural analysis. CryoEM has the potential for broad impact in biomedical research, including basic cell, molecular, and structural biology, and increasingly in drug discovery and vaccine development. Recent advances have led to the expansion of molecular and cellular structure determination at an exponential rate. National and regional centers have emerged to support this growth by increasing the accessibility of cryoEM throughout the biomedical research community. Through cooperation and synergy, these centers form a network of resources that accelerate the adoption of best practices for access and training and establish sustainable workflows to build future research capacity.
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Affiliation(s)
- Christina M. Zimanyi
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Mykhailo Kopylov
- 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
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Correspondence: (E.T. Eng)
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7
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Saibil HR. Cryo-EM in molecular and cellular biology. Mol Cell 2022; 82:274-284. [DOI: 10.1016/j.molcel.2021.12.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022]
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8
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Quinn PD, Alianelli L, Gomez-Gonzalez M, Mahoney D, Cacho-Nerin F, Peach A, Parker JE. The Hard X-ray Nanoprobe beamline at Diamond Light Source. JOURNAL OF SYNCHROTRON RADIATION 2021; 28:1006-1013. [PMID: 33950009 PMCID: PMC8127369 DOI: 10.1107/s1600577521002502] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 03/06/2021] [Indexed: 05/31/2023]
Abstract
The Hard X-ray Nanoprobe beamline, I14, at Diamond Light Source is a new facility for nanoscale microscopy. The beamline was designed with an emphasis on multi-modal analysis, providing elemental mapping, speciation mapping by XANES, structural phase mapping using nano-XRD and imaging through differential phase contrast and ptychography. The 185 m-long beamline operates over a 5 keV to 23 keV energy range providing a ≤50 nm beam size for routine user experiments and a flexible scanning system allowing fast acquisition. The beamline achieves robust and stable operation by imaging the source in the vertical direction and implementing horizontally deflecting primary optics and an overfilled secondary source in the horizontal direction. This paper describes the design considerations, optical layout, aspects of the hardware engineering and scanning system in operation as well as some examples illustrating the beamline performance.
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Affiliation(s)
- Paul D. Quinn
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Lucia Alianelli
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Miguel Gomez-Gonzalez
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - David Mahoney
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Fernando Cacho-Nerin
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Andrew Peach
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Julia E. Parker
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
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9
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Gilbert RJC. Electron microscopy as a critical tool in the determination of pore forming mechanisms in proteins. Methods Enzymol 2021; 649:71-102. [PMID: 33712203 DOI: 10.1016/bs.mie.2021.01.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Electron microscopy has consistently played an important role in the description of pore-forming protein systems. The discovery of pore-forming proteins has depended on visualization of the structural pores formed by their oligomeric protein complexes, and as electron microscopy has advanced technologically so has the degree of insight it has been able to give. This review considers a large number of published studies of pore-forming complexes in prepore and pore states determined using single-particle cryo-electron microscopy. Sample isolation and preparation, imaging and image analysis, structure determination and optimization of results are all discussed alongside challenges which pore-forming proteins particularly present. The review also considers the use made of cryo-electron tomography to study pores within their membrane environment and which will prove an increasingly important approach for the future.
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Affiliation(s)
- Robert J C Gilbert
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
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10
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Umrekar TR, Cohen E, Drobnič T, Gonzalez-Rodriguez N, Beeby M. CryoEM of bacterial secretion systems: A primer for microbiologists. Mol Microbiol 2020; 115:366-382. [PMID: 33140482 DOI: 10.1111/mmi.14637] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 12/11/2022]
Abstract
"CryoEM" has come of age, enabling considerable structural insights into many facets of molecular biology. Here, we present a primer for microbiologists to understand the capabilities and limitations of two complementary cryoEM techniques for studying bacterial secretion systems. The first, single particle analysis, determines the structures of purified protein complexes to resolutions sufficient for molecular modeling, while the second, electron cryotomography and subtomogram averaging, tends to determine more modest resolution structures of protein complexes in intact cells. We illustrate these abilities with examples of insights provided into how secretion systems work by cryoEM, with a focus on type III secretion systems.
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Affiliation(s)
| | - Eli Cohen
- Department of Life Sciences, Imperial College London, London, UK
| | - Tina Drobnič
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, UK
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11
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Quemin ERJ, Machala EA, Vollmer B, Pražák V, Vasishtan D, Rosch R, Grange M, Franken LE, Baker LA, Grünewald K. Cellular Electron Cryo-Tomography to Study Virus-Host Interactions. Annu Rev Virol 2020; 7:239-262. [PMID: 32631159 DOI: 10.1146/annurev-virology-021920-115935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses are obligatory intracellular parasites that reprogram host cells upon infection to produce viral progeny. Here, we review recent structural insights into virus-host interactions in bacteria, archaea, and eukaryotes unveiled by cellular electron cryo-tomography (cryoET). This advanced three-dimensional imaging technique of vitreous samples in near-native state has matured over the past two decades and proven powerful in revealing molecular mechanisms underlying viral replication. Initial studies were restricted to cell peripheries and typically focused on early infection steps, analyzing surface proteins and viral entry. Recent developments including cryo-thinning techniques, phase-plate imaging, and correlative approaches have been instrumental in also targeting rare events inside infected cells. When combined with advances in dedicated image analyses and processing methods, details of virus assembly and egress at (sub)nanometer resolution were uncovered. Altogether, we provide a historical and technical perspective and discuss future directions and impacts of cryoET for integrative structural cell biology analyses of viruses.
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Affiliation(s)
- Emmanuelle R J Quemin
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Emily A Machala
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Benjamin Vollmer
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Vojtěch Pražák
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Daven Vasishtan
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Rene Rosch
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Michael Grange
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Linda E Franken
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Lindsay A Baker
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Kay Grünewald
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
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12
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Sader K, Matadeen R, Castro Hartmann P, Halsan T, Schlichten C. Industrial cryo-EM facility setup and management. Acta Crystallogr D Struct Biol 2020; 76:313-325. [PMID: 32254055 PMCID: PMC7137108 DOI: 10.1107/s2059798320002223] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/17/2020] [Indexed: 11/15/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) has rapidly expanded with the introduction of direct electron detectors, improved image-processing software and automated image acquisition. Its recent adoption by industry, particularly in structure-based drug design, creates new requirements in terms of reliability, reproducibility and throughput. In 2016, Thermo Fisher Scientific (then FEI) partnered with the Medical Research Council Laboratory of Molecular Biology, the University of Cambridge Nanoscience Centre and five pharmaceutical companies [Astex Pharmaceuticals, AstraZeneca, GSK, Sosei Heptares and Union Chimique Belge (UCB)] to form the Cambridge Pharmaceutical Cryo-EM Consortium to share the risks of exploring cryo-EM for early-stage drug discovery. The Consortium expanded with a second Themo Scientific Krios Cryo-EM at the University of Cambridge Department of Materials Science and Metallurgy. Several Consortium members have set up in-house facilities, and a full service cryo-EM facility with Krios and Glacios has been created with the Electron Bio-Imaging Centre for Industry (eBIC for Industry) at Diamond Light Source (DLS), UK. This paper will cover the lessons learned during the setting up of these facilities, including two Consortium Krios microscopes and preparation laboratories, several Glacios microscopes at Consortium member sites, and a Krios and Glacios at eBIC for Industry, regarding site evaluation and selection for high-resolution cryo-EM microscopes, the installation process, scheduling, the operation and maintenance of the microscopes and preparation laboratories, and image processing.
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Affiliation(s)
- Kasim Sader
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Rishi Matadeen
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
- Diamond Light Source, Electron Bio-Imaging Centre for Industry, Oxford, United Kingdom
| | - Pablo Castro Hartmann
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Tor Halsan
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Chris Schlichten
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
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13
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Hey T, Butler K, Jackson S, Thiyagalingam J. Machine learning and big scientific data. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190054. [PMID: 31955675 PMCID: PMC7015290 DOI: 10.1098/rsta.2019.0054] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/06/2019] [Indexed: 05/21/2023]
Abstract
This paper reviews some of the challenges posed by the huge growth of experimental data generated by the new generation of large-scale experiments at UK national facilities at the Rutherford Appleton Laboratory (RAL) site at Harwell near Oxford. Such 'Big Scientific Data' comes from the Diamond Light Source and Electron Microscopy Facilities, the ISIS Neutron and Muon Facility and the UK's Central Laser Facility. Increasingly, scientists are now required to use advanced machine learning and other AI technologies both to automate parts of the data pipeline and to help find new scientific discoveries in the analysis of their data. For commercially important applications, such as object recognition, natural language processing and automatic translation, deep learning has made dramatic breakthroughs. Google's DeepMind has now used the deep learning technology to develop their AlphaFold tool to make predictions for protein folding. Remarkably, it has been able to achieve some spectacular results for this specific scientific problem. Can deep learning be similarly transformative for other scientific problems? After a brief review of some initial applications of machine learning at the RAL, we focus on challenges and opportunities for AI in advancing materials science. Finally, we discuss the importance of developing some realistic machine learning benchmarks using Big Scientific Data coming from several different scientific domains. We conclude with some initial examples of our 'scientific machine learning' benchmark suite and of the research challenges these benchmarks will enable. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'.
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Affiliation(s)
- Tony Hey
- Scientific Computing Department, Rutherford Appleton Laboratory, Science and Technology Facilities Council, Didcot OX11 0QX, UK
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14
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Zivanov J, Nakane T, Scheres SHW. Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1. IUCRJ 2020; 7:253-267. [PMID: 32148853 PMCID: PMC7055373 DOI: 10.1107/s2052252520000081] [Citation(s) in RCA: 443] [Impact Index Per Article: 110.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/06/2020] [Indexed: 05/21/2023]
Abstract
Methods are presented that detect three types of aberrations in single-particle cryo-EM data sets: symmetrical and antisymmetrical optical aberrations and magnification anisotropy. Because these methods only depend on the availability of a preliminary 3D reconstruction from the data, they can be used to correct for these aberrations for any given cryo-EM data set, a posteriori. Using five publicly available data sets, it is shown that considering these aberrations improves the resolution of the 3D reconstruction when these effects are present. The methods are implemented in version 3.1 of the open-source software package RELION.
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Affiliation(s)
- Jasenko Zivanov
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, England
- Biozentrum, University of Basel, Switzerland
| | - Takanori Nakane
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - Sjors H. W. Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, England
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15
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Integrative Structural Biology of Protein-RNA Complexes. Structure 2020; 28:6-28. [DOI: 10.1016/j.str.2019.11.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/17/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022]
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16
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Rivera-Calzada A, Carroni M. Editorial: Technical Advances in Cryo-Electron Microscopy. Front Mol Biosci 2019; 6:72. [PMID: 31508425 PMCID: PMC6713907 DOI: 10.3389/fmolb.2019.00072] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/07/2019] [Indexed: 11/13/2022] Open
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17
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Kandiah E, Giraud T, de Maria Antolinos A, Dobias F, Effantin G, Flot D, Hons M, Schoehn G, Susini J, Svensson O, Leonard GA, Mueller-Dieckmann C. CM01: a facility for cryo-electron microscopy at the European Synchrotron. Acta Crystallogr D Struct Biol 2019; 75:528-535. [PMID: 31205015 PMCID: PMC6580229 DOI: 10.1107/s2059798319006880] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/13/2019] [Indexed: 12/31/2022] Open
Abstract
Recent improvements in direct electron detectors, microscope technology and software provided the stimulus for a `quantum leap' in the application of cryo-electron microscopy in structural biology, and many national and international centres have since been created in order to exploit this. Here, a new facility for cryo-electron microscopy focused on single-particle reconstruction of biological macromolecules that has been commissioned at the European Synchrotron Radiation Facility (ESRF) is presented. The facility is operated by a consortium of institutes co-located on the European Photon and Neutron Campus and is managed in a similar fashion to a synchrotron X-ray beamline. It has been open to the ESRF structural biology user community since November 2017 and will remain open during the 2019 ESRF-EBS shutdown.
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Affiliation(s)
- Eaazhisai Kandiah
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Thierry Giraud
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042 Grenoble, France
| | | | - Fabien Dobias
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Gregory Effantin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - David Flot
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Michael Hons
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Guy Schoehn
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Jean Susini
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Olof Svensson
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Gordon A. Leonard
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38042 Grenoble, France
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18
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Gómez-Blanco J, de la Rosa-Trevín JM, Marabini R, Del Cano L, Jiménez A, Martínez M, Melero R, Majtner T, Maluenda D, Mota J, Rancel Y, Ramírez-Aportela E, Vilas JL, Carroni M, Fleischmann S, Lindahl E, Ashton AW, Basham M, Clare DK, Savage K, Siebert CA, Sharov GG, Sorzano COS, Conesa P, Carazo JM. Using Scipion for stream image processing at Cryo-EM facilities. J Struct Biol 2018; 204:457-463. [PMID: 30296492 PMCID: PMC6303188 DOI: 10.1016/j.jsb.2018.10.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022]
Abstract
Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed a modular workflow system called Scipion (de la Rosa-Trevín et al., 2016). We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detailed evaluation of the data quality before the acquisition is finished. At present, Scipion has been deployed and is in production mode in seven Cryo-EM facilities throughout the world.
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Affiliation(s)
- J Gómez-Blanco
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
| | - J M de la Rosa-Trevín
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - R Marabini
- Escuela Politécnica Superior, Universidad Autónoma de Madrid, 28049 Cantoblanco, Madrid, Spain.
| | - L Del Cano
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - A Jiménez
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - M Martínez
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - R Melero
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - T Majtner
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - D Maluenda
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - J Mota
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - Y Rancel
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - E Ramírez-Aportela
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - J L Vilas
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - M Carroni
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - S Fleischmann
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - E Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden; Swedish e-Science Research Center, KTH Royal Institute of Technology, Stockholm, Sweden
| | - A W Ashton
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - M Basham
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - D K Clare
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - K Savage
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - C A Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - G G Sharov
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 OQH, United Kingdom
| | - C O S Sorzano
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - P Conesa
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
| | - J M Carazo
- Biocomputing Unit, National Center for Biotechnology (CSIC), C/ Darwin, 3, Campus Universidad Autónoma, 28049 Cantoblanco, Madrid, Spain
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Grimes JM, Hall DR, Ashton AW, Evans G, Owen RL, Wagner A, McAuley KE, von Delft F, Orville AM, Sorensen T, Walsh MA, Ginn HM, Stuart DI. Where is crystallography going? Acta Crystallogr D Struct Biol 2018; 74:152-166. [PMID: 29533241 PMCID: PMC5947779 DOI: 10.1107/s2059798317016709] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 11/20/2017] [Indexed: 11/28/2022] Open
Abstract
Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and cryo-crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments. In addition, X-ray free-electron lasers offer to capture fragments of reciprocal space without radiation damage, and open up the subpicosecond regime of protein dynamics and activity. But electrons have recently stolen the limelight: so is X-ray crystallography in rude health, or will imaging methods, especially single-particle electron microscopy, render it obsolete for the most interesting biology, whilst electron diffraction enables structure determination from even the smallest crystals? We will lay out some information to help you decide.
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Affiliation(s)
- Jonathan M. Grimes
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
| | - David R. Hall
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Alun W. Ashton
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Gwyndaf Evans
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Robin L. Owen
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Armin Wagner
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Katherine E. McAuley
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Frank von Delft
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, England
| | - Allen M. Orville
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Thomas Sorensen
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Martin A. Walsh
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, England
| | - Helen M. Ginn
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
| | - David I. Stuart
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, England
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20
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Baker LA, Grange M, Grünewald K. Electron cryo-tomography captures macromolecular complexes in native environments. Curr Opin Struct Biol 2017; 46:149-156. [DOI: 10.1016/j.sbi.2017.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/21/2017] [Accepted: 08/23/2017] [Indexed: 11/27/2022]
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