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cryo electron tomography

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https://www.readbyqxmd.com/read/28735108/structural-biology-outside-the-box-inside-the-cell
#1
REVIEW
Jürgen M Plitzko, Benjamin Schuler, Philipp Selenko
Recent developments in cellular cryo-electron tomography, in-cell single-molecule Förster resonance energy transfer-spectroscopy, nuclear magnetic resonance-spectroscopy and electron paramagnetic resonance-spectroscopy delivered unprecedented insights into the inner workings of cells. Here, we review complementary aspects of these methods and provide an outlook toward joint applications in the future.
July 20, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28733815/structure-of-isolated-z-disks-from-honeybee-flight-muscle
#2
Mara Rusu, Zhongjun Hu, Kenneth A Taylor, John Trinick
The Z-disk is a complex structure comprising some 40 proteins that are involved in the transmission of force developed during muscle contraction and in important signalling pathways that govern muscle homeostasis. In the Z-disk the ends of antiparallel thin filaments from adjacent sarcomeres are crosslinked by α-actinin. The structure of the Z-disk lattice varies greatly throughout the animal kingdom. In vertebrates the thin filaments form a tetragonal lattice, whereas invertebrate flight muscle has a hexagonal lattice...
July 21, 2017: Journal of Muscle Research and Cell Motility
https://www.readbyqxmd.com/read/28726246/cryo-electron-tomography-the-cell-biology-that-came-in-from-the-cold
#3
REVIEW
Jonathan Wagner, Miroslava Schaffer, Rubén Fernández-Busnadiego
Cryo-electron tomography (cryo-ET) provides high resolution 3D views into cells pristinely preserved by vitrification. Recent technical advances such as direct electron detectors, the Volta phase plate and cryo-focused ion beam milling have dramatically pushed image quality and expanded the range of cryo-ET applications. Cryo-ET not only allows mapping the positions and interactions of macromolecules within their intact cellular context, but can also reveal their in situ structure at increasing resolution. Here, we review how recent work using cutting-edge cryo-ET technologies is starting to provide fresh views into different aspects of cellular biology at an unprecedented level of detail...
July 20, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28699890/changes-of-mitochondrial-ultrastructure-and-function-during-ageing-in-mice-and-drosophila
#4
Tobias Brandt, Arnaud Mourier, Luke S Tain, Linda Partridge, Nils-Göran Larsson, Werner Kühlbrandt
Ageing is a progressive decline of intrinsic physiological functions. We examined the impact of ageing on the ultrastructure and function of mitochondria in mouse and fruit flies (Drosophila melanogaster) by electron cryo-tomography and respirometry and discovered distinct age-related changes in both model organisms. Mitochondrial function and ultrastructure are maintained in mouse heart, whereas subpopulations of mitochondria from mouse liver show age-related changes in membrane morphology. Subpopulations of mitochondria from young and old mouse kidney resemble those described for apoptosis...
July 12, 2017: ELife
https://www.readbyqxmd.com/read/28675816/expanding-the-boundaries-of-cryo-em-with-phase-plates
#5
REVIEW
Radostin Danev, Wolfgang Baumeister
Phase plates have long been considered as a means for improving the performance of cryo-electron microscopy (cryo-EM). But practical limitations, such as a short lifespan or cumbersome usage have prevented their widespread adoption. The recently developed Volta phase plate overcomes most of the practical issues and it is now commercially available. Results from both, electron cryo-tomography (cryo-ET) and single particle analysis (SPA), have demonstrated the benefits of using a phase plate. In CET phase plates have helped to visualize cellular ultrastructure in unprecedented detail...
July 1, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28671286/structural-characterization-of-the-nap-the-major-adhesion-complex-of-the-human-pathogen-mycoplasma-genitalium
#6
Margot P Scheffer, Luis Gonzalez-Gonzalez, Anja Seybert, Mercè Ratera, Michael Kunz, José M Valpuesta, Ignacio Fita, Enrique Querol, Jaume Piñol, Jaime Martín-Benito, Achilleas S Frangakis
Mycoplasma genitalium, the causative agent of non-gonococcal urethritis and pelvic inflammatory disease in humans, is a small eubacterium that lacks a peptidoglycan cell wall. On the surface of its plasma membrane is the major surface adhesion complex, known as NAP, that is essential for adhesion and gliding motility of the organism. Here, we have performed cryo-electron tomography of intact cells and detergent permeabilized M. genitalium cell aggregates, providing sub-tomogram averages of free and cell-attached NAPs respectively, revealing a tetrameric complex with two-fold rotational (C2) symmetry...
July 3, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28653620/cryo-electron-tomography-reveals-novel-features-of-a-viral-rna-replication-compartment
#7
Kenneth J Ertel, Desirée Benefield, Daniel Castaño-Diez, Janice G Pennington, Mark Horswill, Johan A den Boon, Marisa S Otegui, Paul Ahlquist
Positive-strand RNA viruses, the largest genetic class of viruses, include numerous important pathogens such as Zika virus. These viruses replicate their RNA genomes in novel, membrane-bounded mini-organelles, but the organization of viral proteins and RNAs in these compartments has been largely unknown. We used cryo-electron tomography to reveal many previously unrecognized features of Flock house nodavirus (FHV) RNA replication compartments. These spherular invaginations of outer mitochondrial membranes are packed with electron-dense RNA fibrils and their volumes are closely correlated with RNA replication template length...
June 27, 2017: ELife
https://www.readbyqxmd.com/read/28637765/electrostatic-interaction-between-polyglutamylated-tubulin-and-the-nexin-dynein-regulatory-complex-regulates-flagellar-motility
#8
Tomohiro Kubo, Toshiyuki Oda
Tubulins undergo various posttranslational modifications. Among them, polyglutamylation is involved in the motility of eukaryotic flagella and the stability of the axonemal microtubules. However, it remains unclear where polyglutamylated tubulin localizes precisely within the axoneme, and how tubulin polyglutamylation affects the flagellar motility. In this study, we identified the three-dimensional (3D) localization of the polyglutamylated tubulin in Chlamydomonas flagella using antibody labeling and cryo-electron tomography...
June 21, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28635493/the-structure-of-lamin-filaments-in-somatic-cells-as-revealed-by-cryo-electron-tomography
#9
Y Turgay, O Medalia
Metazoan nuclei are equipped with nuclear lamina - a thin layer of intermediate filaments (IFs) mostly built of nuclear lamins facing the inner nuclear membrane (INM). The nuclear lamina serves as an interaction hub for INM-proteins, soluble nuclear factors and DNA. It confers structural and mechanical stability to the nucleus, transduces mechanical forces and biochemical signals across the nuclear envelope (NE) and regulates the organization of chromatin. By using cryo-electron tomography (cryo-ET), we recently provided an unprecedented view into the 3D organization of lamin filaments within the lamina meshwork in mammalian somatic cells...
June 21, 2017: Nucleus
https://www.readbyqxmd.com/read/28630150/cryo-electron-tomography-an-ideal-method-to-study-membrane-associated-proteins
#10
REVIEW
Michelle A Dunstone, Alex de Marco
Cryo-electron tomography (cryo-ET) is a three-dimensional imaging technique that makes it possible to analyse the structure of complex and dynamic biological assemblies in their native conditions. The latest technological and image processing developments demonstrate that it is possible to obtain structural information at nanometre resolution. The sample preparation required for the cryo-ET technique does not require the isolation of a protein and other macromolecular complexes from its native environment. Therefore, cryo-ET is emerging as an important tool to study the structure of membrane-associated proteins including pores...
August 5, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/28621666/9%C3%A3-structure-of-the-copi-coat-reveals-that-the-arf1-gtpase-occupies-two-contrasting-molecular-environments
#11
Svetlana O Dodonova, Patrick Aderhold, Juergen Kopp, Iva Ganeva, Simone Röhling, Wim J H Hagen, Irmgard Sinning, Felix Wieland, John A G Briggs
COPI coated vesicles mediate trafficking within the Golgi apparatus and between the Golgi and the endoplasmic reticulum. Assembly of a COPI coated vesicle is initiated by the small GTPase Arf1 that recruits the coatomer complex to the membrane, triggering polymerization and budding. The vesicle uncoats before fusion with a target membrane. Coat components are structurally conserved between COPI and clathrin/adaptor proteins. Using cryo-electron tomography and subtomogram averaging, we determined the structure of the COPI coat assembled on membranes in vitro at 9 Å resolution...
June 16, 2017: ELife
https://www.readbyqxmd.com/read/28611252/the-primary-enveloped-virion-of-herpes-simplex-virus-1-its-role-in-nuclear-egress
#12
William W Newcomb, Juan Fontana, Dennis C Winkler, Naiqian Cheng, J Bernard Heymann, Alasdair C Steven
Many viruses migrate between different cellular compartments for successive stages of assembly. The HSV-1 capsid assembles in the nucleus and then transfers into the cytoplasm. First, the capsid buds through the inner nuclear membrane, becoming coated with nuclear egress complex (NEC) protein. This yields a primary enveloped virion (PEV) whose envelope fuses with the outer nuclear membrane, releasing the capsid into the cytoplasm. We investigated the associated molecular mechanisms by isolating PEVs from US3-null-infected cells and imaging them by cryo-electron microscopy and tomography...
June 13, 2017: MBio
https://www.readbyqxmd.com/read/28609782/influence-of-dna-sequence-on-the-structure-of-minicircles-under-torsional-stress
#13
Qian Wang, Rossitza N Irobalieva, Wah Chiu, Michael F Schmid, Jonathan M Fogg, Lynn Zechiedrich, B Montgomery Pettitt
The sequence dependence of the conformational distribution of DNA under various levels of torsional stress is an important unsolved problem. Combining theory and coarse-grained simulations shows that the DNA sequence and a structural correlation due to topology constraints of a circle are the main factors that dictate the 3D structure of a 336 bp DNA minicircle under torsional stress. We found that DNA minicircle topoisomers can have multiple bend locations under high torsional stress and that the positions of these sharp bends are determined by the sequence, and by a positive mechanical correlation along the sequence...
June 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28601688/structure-and-organization-of-paramyxovirus-particles
#14
REVIEW
Robert M Cox, Richard K Plemper
The paramyxovirus family comprises major human and animal pathogens such as measles virus (MeV), mumps virus (MuV), the parainfluenzaviruses, Newcastle disease virus (NDV), and the highly pathogenic zoonotic hendra (HeV) and nipah (NiV) viruses. Paramyxovirus particles are pleomorphic, with a lipid envelope, nonsegmented RNA genomes of negative polarity, and densely packed glycoproteins on the virion surface. A number of crystal structures of different paramyxovirus proteins and protein fragments were solved, but the available information concerning overall virion organization remains limited...
June 8, 2017: Current Opinion in Virology
https://www.readbyqxmd.com/read/28580912/trends-in-the-electron-microscopy-data-bank-emdb
#15
Ardan Patwardhan
Recent technological advances, such as the introduction of the direct electron detector, have transformed the field of cryo-EM and the landscape of molecular and cellular structural biology. This study analyses these trends from the vantage point of the Electron Microscopy Data Bank (EMDB), the public archive for three-dimensional EM reconstructions. Over 1000 entries were released in 2016, representing almost a quarter of the total number of entries (4431). Structures at better than 6 Å resolution now represent one of the fastest-growing categories, while the share of annually released tomography-related structures is approaching 20%...
June 1, 2017: Acta Crystallographica. Section D, Structural Biology
https://www.readbyqxmd.com/read/28575072/assembly-maturation-and-three-dimensional-helical-structure-of-the-teratogenic-rubella-virus
#16
Vidya Mangala Prasad, Thomas Klose, Michael G Rossmann
Viral infections during pregnancy are a significant cause of infant morbidity and mortality. Of these, rubella virus infection is a well-substantiated example that leads to miscarriages or severe fetal defects. However, structural information about the rubella virus has been lacking due to the pleomorphic nature of the virions. Here we report a helical structure of rubella virions using cryo-electron tomography. Sub-tomogram averaging of the surface spikes established the relative positions of the viral glycoproteins, which differed from the earlier icosahedral models of the virus...
June 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28559166/cryo-fib-specimen-preparation-for-use-in-a-cartridge-type-cryo-tem
#17
Jie He, Chyongere Hsieh, Yongping Wu, Thomas Schmelzer, Pan Wang, Ying Lin, Michael Marko, Haixin Sui
Cryo-electron tomography (cryo-ET) is a well-established technique for studying 3D structural details of subcellular macromolecular complexes and organelles in their nearly native context in the cell. A primary limitation of the application of cryo-ET is the accessible specimen thickness, which is less than the diameters of almost all eukaryotic cells. It has been shown that focused ion beam (FIB) milling can be used to prepare thin, distortion-free lamellae of frozen biological material for high-resolution cryo-ET...
May 27, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28552576/tomominer-and-tomominercloud-a-software-platform-for-large-scale-subtomogram-structural-analysis
#18
Zachary Frazier, Min Xu, Frank Alber
Cryo-electron tomography (cryo-ET) captures the 3D electron density distribution of macromolecular complexes in close to native state. With the rapid advance of cryo-ET acquisition technologies, it is possible to generate large numbers (>100,000) of subtomograms, each containing a macromolecular complex. Often, these subtomograms represent a heterogeneous sample due to variations in the structure and composition of a complex in situ form or because particles are a mixture of different complexes. In this case subtomograms must be classified...
June 6, 2017: Structure
https://www.readbyqxmd.com/read/28551375/cytoskeletal-organization-in-microtentacles
#19
Alison N Killilea, Roseann Csencsits, Emily Le, Anand M Patel, Samuel J Kenny, Ke Xu, Kenneth H Downing
Microtentacles are thin, flexible cell protrusions that have recently been described and whose presence enhances efficient attachment of circulating cells. They are found on circulating tumor cells and can be induced on a wide range of breast cancer cell lines, where they are promoted by factors that either stabilize microtubules or destabilize the actin cytoskeleton. Evidence suggests that they are relevant to the metastatic spread of cancer, so understanding their structure and formation may lead to useful therapies...
May 24, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28541401/three-dimensional-structural-labeling-microscopy-of-cilia-and-flagella
#20
Toshiyuki Oda
Locating a molecule within a cell using protein-tagging and immunofluorescence is a fundamental technique in cell biology, whereas in three-dimensional electron microscopy, locating a subunit within a macromolecular complex remains challenging. Recently, we developed a new structural labeling method for cryo-electron tomography by taking advantage of the biotin-streptavidin system, and have intensively used this method to locate a number of proteins and protein domains in cilia and flagella. In this review, we summarize our findings on the three-dimensional architecture of the axoneme, especially the importance of coiled-coil proteins...
May 25, 2017: Microscopy
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