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https://www.readbyqxmd.com/read/27882950/neutralization-mechanism-of-a-highly-potent-antibody-against-zika-virus
#1
Shuijun Zhang, Victor A Kostyuchenko, Thiam-Seng Ng, Xin-Ni Lim, Justin S G Ooi, Sebastian Lambert, Ter Yong Tan, Douglas G Widman, Jian Shi, Ralph S Baric, Shee-Mei Lok
The rapid spread of Zika virus (ZIKV), which causes microcephaly and Guillain-Barré syndrome, signals an urgency to identify therapeutics. Recent efforts to rescreen dengue virus human antibodies for ZIKV cross-neutralization activity showed antibody C10 as one of the most potent. To investigate the ability of the antibody to block fusion, we determined the cryoEM structures of the C10-ZIKV complex at pH levels mimicking the extracellular (pH8.0), early (pH6.5) and late endosomal (pH5.0) environments. The 4...
November 24, 2016: Nature Communications
https://www.readbyqxmd.com/read/27852863/cryoem-structures-of-expanded-poliovirus-with-vhhs-sample-the-conformational-repertoire-of-the-expanded-state
#2
Mike Strauss, Lise Schotte, Krishanthi S Karunatilaka, David J Filman, James M Hogle
: Using cryoelectron microscopy, expanded 80S-like poliovirions were visualized in complexes with four 80S-specific camelid VHHs (Nanobodies®). In all four complexes, the VHHs bind to a site on the top surface of capsid protein VP3, which is hidden in native virus. Interestingly, although the four VHHs bind to the same site, the structures of the expanded virus differ in detail in each complex, suggesting that each of the nanobodies has sampled a range of low energy structures available to the expanded virion...
November 16, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27834216/schizosaccharomyces-pombe-kinesin-5-switches-direction-using-a-steric-blocking-mechanism
#3
Mishan Britto, Adeline Goulet, Syeda Rizvi, Ottilie von Loeffelholz, Carolyn A Moores, Robert A Cross
Cut7, the sole kinesin-5 in Schizosaccharomyces pombe, is essential for mitosis. Like other yeast kinesin-5 motors, Cut7 can reverse its stepping direction, by mechanisms that are currently unclear. Here we show that for full-length Cut7, the key determinant of stepping direction is the degree of motor crowding on the microtubule lattice, with greater crowding converting the motor from minus end-directed to plus end-directed stepping. To explain how high Cut7 occupancy causes this reversal, we postulate a simple proximity sensing mechanism that operates via steric blocking...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27752045/structures-and-stabilization-of-kinetoplastid-specific-split-rrnas-revealed-by-comparing-leishmanial-and-human-ribosomes
#4
Xing Zhang, Mason Lai, Winston Chang, Iris Yu, Ke Ding, Jan Mrazek, Hwee L Ng, Otto O Yang, Dmitri A Maslov, Z Hong Zhou
The recent success in ribosome structure determination by cryoEM has opened the door to defining structural differences between ribosomes of pathogenic organisms and humans and to understand ribosome-targeting antibiotics. Here, by direct electron-counting cryoEM, we have determined the structures of the Leishmania donovani and human ribosomes at 2.9 Å and 3.6 Å, respectively. Our structure of the leishmanial ribosome elucidates the organization of the six fragments of its large subunit rRNA (as opposed to a single 28S rRNA in most eukaryotes, including humans) and reveals atomic details of a unique 20 amino acid extension of the uL13 protein that pins down the ends of three of the rRNA fragments...
October 18, 2016: Nature Communications
https://www.readbyqxmd.com/read/27701014/microed-opens-a-new-era-for-biological-structure-determination
#5
Brent L Nannenga, Tamir Gonen
In 2013 we unveiled the cryo-electron microscopy (CryoEM) method of MicroED, or three-dimensional (3D) electron diffraction of microscopic crystals. Here tiny 3D crystals of biological material are used in an electron microscope for diffraction data collection under cryogenic conditions. The data is indexed, integrated, merged and scaled using standard X-ray crystallography software to determine structures at atomic resolution. In this review we provide an overview of the MicroED method and compare it with other CryoEM methods...
October 1, 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27693469/cryo-em-structure-of-respiratory-complex-i-reveals-a-link-to-mitochondrial-sulfur-metabolism
#6
Edoardo D'Imprima, Deryck J Mills, Kristian Parey, Ulrich Brandt, Werner Kühlbrandt, Volker Zickermann, Janet Vonck
Mitochondrial complex I is a 1MDa membrane protein complex with a central role in aerobic energy metabolism. The bioenergetic core functions are executed by 14 central subunits that are conserved from bacteria to man. Despite recent progress in structure determination, our understanding of the function of the ~30 accessory subunits associated with the mitochondrial complex is still limited. We have investigated the structure of complex I from the aerobic yeast Yarrowia lipolytica by cryo-electron microscopy...
December 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27687475/structures-of-the-colossal-ryr1-calcium-release-channel
#7
Oliver B Clarke, Wayne A Hendrickson
Ryanodine receptors (RyRs) are intracellular cation channels that mediate the rapid and voluminous release of Ca(2+) from the sarcoplasmic reticulum (SR) as required for excitation-contraction coupling in cardiac and skeletal muscle. Understanding of the architecture and gating of RyRs has advanced dramatically over the past two years, due to the publication of high resolution cryo-electron microscopy (cryoEM) reconstructions and associated atomic models of multiple functional states of the skeletal muscle receptor, RyR1...
August 2016: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/27671094/a-guide-to-the-3d-structure-of-the-ryanodine-receptor-type-1-by-cryoem
#8
Montserrat Samsó
Signal transduction by the ryanodine receptor (RyR) is essential in many excitable cells including all striated contractile cells and some types of neurons. While its transmembrane domain is a classic tetrameric, six-transmembrane cation channel, the cytoplasmic domain is uniquely large and complex, hosting a multiplicity of specialized domains. The overall outline and substructure readily recognizable by electron microscopy make RyR a geometrically well-behaved specimen. Hence, for the last two decades, the 3D structural study of the RyR has tracked closely the technological advances in electron microscopy, cryo-electron microscopy (cryoEM), and computerized 3D reconstruction...
September 27, 2016: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/27662086/large-scale-movements-of-if3-and-trna-during-bacterial-translation-initiation
#9
Tanweer Hussain, Jose L Llácer, Brian T Wimberly, Jeffrey S Kieft, V Ramakrishnan
In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1-3, representing different steps along the initiation pathway. IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities. IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA...
September 22, 2016: Cell
https://www.readbyqxmd.com/read/27658821/single-particle-electron-cryomicroscopy-trends-issues-and-future-perspective
#10
Kutti R Vinothkumar, Richard Henderson
There has been enormous progress during the last few years in the determination of three-dimensional biological structures by single particle electron cryomicroscopy (cryoEM), allowing maps to be obtained with higher resolution and from fewer images than required previously. This is due principally to the introduction of a new type of direct electron detector that has 2- to 3-fold higher detective quantum efficiency than available previously, and to the improvement of the computational algorithms for image processing...
January 2016: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/27644322/mechanism-for-nuclease-regulation-in-recbcd
#11
Martin Wilkinson, Yuriy Chaban, Dale B Wigley
In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is catalysed by AddAB, AdnAB or RecBCD-type helicase-nucleases. These enzyme complexes are highly processive, duplex unwinding and degrading machines that require tight regulation. Here, we report the structure of E.coli RecBCD, determined by cryoEM at 3.8 Å resolution, with a DNA substrate that reveals how the nuclease activity of the complex is activated once unwinding progresses. Extension of the 5'-tail of the unwound duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit...
2016: ELife
https://www.readbyqxmd.com/read/27616740/the-infectious-particle-of-insect-borne-totivirus-like-omono-river-virus-has-raised-ridges-and-lacks-fibre-complexes
#12
Kenta Okamoto, Naoyuki Miyazaki, Daniel S D Larsson, Daisuke Kobayashi, Martin Svenda, Kerstin Mühlig, Filipe R N C Maia, Laura H Gunn, Haruhiko Isawa, Mutsuo Kobayashi, Kyoko Sawabe, Kazuyoshi Murata, Janos Hajdu
Omono River virus (OmRV) is a double-stranded RNA virus isolated from Culex mosquitos, and it belongs to a group of unassigned insect viruses that appear to be related to Totiviridae. This paper describes electron cryo-microscopy (cryoEM) structures for the intact OmRV virion to 8.9 Å resolution and the structure of the empty virus-like-particle, that lacks RNA, to 8.3 Å resolution. The icosahedral capsid contains 120-subunits and resembles another closely related arthropod-borne totivirus-like virus, the infectious myonecrosis virus (IMNV) from shrimps...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27581981/releasing-the-genomic-rna-sequestered-in-the-mumps-virus-nucleocapsid
#13
Chelsea Severin, James R Terrell, James R Zengel, Robert Cox, Richard K Plemper, Biao He, Ming Luo
: In a negative strand RNA virus, the genomic RNA is sequestered inside the nucleocapsid when the viral RNA-dependent RNA polymerase uses it as the template for viral RNA synthesis. It must require a conformational change in the nucleocapsid protein (NP) to make the RNA accessible by the viral polymerase during this process. The structure of an empty mumps virus nucleocapsid-like particle is determined to 10.4 Å resolution by cryoEM image reconstruction. By modeling the crystal structure of parainfluenza virus 5 into the density, it is shown that the α-helix close to the RNA became flexible when RNA was removed...
August 31, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27572735/databases-and-archiving-for-cryoem
#14
A Patwardhan, C L Lawson
CryoEM in structural biology is currently served by three public archives-EMDB for 3DEM reconstructions, PDB for models built from 3DEM reconstructions, and EMPIAR for the raw 2D image data used to obtain the 3DEM reconstructions. These archives play a vital role for both the structural community and the wider biological community in making the data accessible so that results may be reused, reassessed, and integrated with other structural and bioinformatics resources. The important role of the archives is underpinned by the fact that many journals mandate the deposition of data to PDB and EMDB on publication...
2016: Methods in Enzymology
https://www.readbyqxmd.com/read/27572730/tools-for-model-building-and-optimization-into-near-atomic-resolution-electron-cryo-microscopy-density-maps
#15
F DiMaio, W Chiu
Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described...
2016: Methods in Enzymology
https://www.readbyqxmd.com/read/27572727/single-particle-refinement-and-variability-analysis-in-eman2-1
#16
S J Ludtke
CryoEM single-particle reconstruction has been growing rapidly over the last 3 years largely due to the development of direct electron detectors, which have provided data with dramatic improvements in image quality. It is now possible in many cases to produce near-atomic resolution structures, and yet 2/3 of published structures remain at substantially lower resolutions. One important cause for this is compositional and conformational heterogeneity, which is both a resolution-limiting factor and presenting a unique opportunity to better relate structure to function...
2016: Methods in Enzymology
https://www.readbyqxmd.com/read/27572724/strategies-for-automated-cryoem-data-collection-using-direct-detectors
#17
A Cheng, Y Z Tan, V P Dandey, C S Potter, B Carragher
The new generation of direct electron detectors has been a major contributor to the recent resolution revolution in cryo-electron microscopy. Optimal use of these new cameras using automated data collection software is critical for high-throughput near-atomic resolution cryo-electron microscopy research. We present an overview of the practical aspects of automated data collection in the context of this new generation of direct detectors, highlighting the differences, challenges, and opportunities the new detectors provide compared to the previous generation of data acquisition media...
2016: Methods in Enzymology
https://www.readbyqxmd.com/read/27572721/direct-electron-detectors
#18
G McMullan, A R Faruqi, R Henderson
Direct electron detectors have played a key role in the recent increase in the power of single-particle electron cryomicroscopy (cryoEM). In this chapter, we summarize the background to these recent developments, give a practical guide to their optimal use, and discuss future directions.
2016: Methods in Enzymology
https://www.readbyqxmd.com/read/27531956/structural-conservation-in-the-template-pseudoknot-domain-of-vertebrate-telomerase-rna-from-teleost-fish-to-human
#19
Yaqiang Wang, Joseph D Yesselman, Qi Zhang, Mijeong Kang, Juli Feigon
Telomerase is an RNA-protein complex that includes a unique reverse transcriptase that catalyzes the addition of single-stranded telomere DNA repeats onto the 3' ends of linear chromosomes using an integral telomerase RNA (TR) template. Vertebrate TR contains the template/pseudoknot (t/PK) and CR4/5 domains required for telomerase activity in vitro. All vertebrate pseudoknots include two subdomains: P2ab (helices P2a and P2b with a 5/6-nt internal loop) and the minimal pseudoknot (P2b-P3 and associated loops)...
August 30, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27452773/atomic-resolution-structure-determination-by-the-cryo-em-method-microed
#20
Liu Shian, Hattne Johan, Reyes E Francis, Sanchez-Martinez Silvia, M Jason de la Cruz, D Shi, T Gonen
The electron cryo-microscopy (cryoEM) method MicroED has been rapidly developing. In this review we highlight some of the key steps in MicroED from crystal analysis to structure determination. We compare and contrast MicroED and the latest X-ray based diffraction method the X-ray free electron laser (XFEL). Strengths and shortcomings of both MicroED and XFEL are discussed. Finally, all current MicroED structures are tabulated with a view to the future. This article is protected by copyright. All rights reserved...
July 25, 2016: Protein Science: a Publication of the Protein Society
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