Abstract:
:The QVIEW image-processing software package provides a graphical user interface for interactive and rapid selection of particles from digital electron micrographs. This package was developed to facilitate the selection of elliptical, hydrophobic, and aggregating particles, which present complications for other particle selection packages. Speed improvements have been attained by using the fast graphics routines available in the Tc1/Tk toolkit and by separating the time consuming image-processing procedures from the interactive selection steps. The software is based on C++ and Tc1/Tk, both of which are readily available on many computer platforms. Processing features include removal of oversaturated pixels, planar subtraction using three or more background regions, exclusion of unwanted density such as nearby particles, and application of a circular or elliptical mask. Particles, along with their corresponding background and exclude regions, may be selected interactively from multiple digital micrographs, and the selection parameters are saved in a disk file for later processing. C shell processing scripts are easily modified and customized for specific applications. In summary, this software package enables the user-friendly, rapid selection of particles suitable for input into three-dimensional reconstruction packages.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Shah AK,Stewart PLdoi
10.1006/jsbi.1998.4011subject
Has Abstractpub_date
1998-09-01 00:00:00pages
17-21issue
1eissn
1047-8477issn
1095-8657pii
S1047-8477(98)94011-4journal_volume
123pub_type
杂志文章abstract::A defining property of a crystal is its symmetry. This mini-review sets out to summarize all aspects that define 2D crystallographic symmetry as applied to the study of macromolecular structure. It begins by defining molecular point symmetries, before covering crystallographic symmetry operations in 2D, common notatio...
journal_title:Journal of structural biology
pub_type: 杂志文章,评审
doi:10.1016/j.jsb.2007.07.002
更新日期:2007-12-01 00:00:00
abstract::Sialic acid residues found as terminal monosaccharides in various types of glycan chains in cell surface glycoproteins and glycolipids have been identified as important contributors of cell-cell interactions in normal vs. abnormal cellular behavior and are pivotal in diseases such as cancers. In vertebrates, sialic ac...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2020.107628
更新日期:2020-11-01 00:00:00
abstract::Staphylococcus aureus hibernation promoting factor (SaHPF) is responsible for the formation of 100S ribosome dimers, which in turn help this pathogen to reduce energy spent under unfavorable conditions. Ribosome dimer formation strongly depends on the dimerization of the C-terminal domain of SaHPF (CTDSaHPF). In this ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2019.107408
更新日期:2020-01-01 00:00:00
abstract::To characterize the spatial and temporal occurrence of programmed cell death (PCD) in Lilium anther tissues, we used both microscopical and molecular markers of apoptosis for developmental stages from meiosis to pollen release. The first hallmarks of PCD include cell condensation and shrinkage of the cytoplasm, separa...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2005.07.011
更新日期:2005-11-01 00:00:00
abstract::Cryo-electron tomography (cryo-ET) provides three-dimensional (3D) structural information of bacteria preserved in a native, frozen-hydrated state. The typical low contrast of tilt-series images, a result of both the need for a low electron dose and the use of conventional defocus phase-contrast imaging, is a challeng...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2013.09.011
更新日期:2014-01-01 00:00:00
abstract::Bacterial two-component regulatory systems (TCS) play important roles in sensing environmental stimuli and responding to them by regulating gene expression. VbrK/VbrR, a TCS in Vibrio parahaemolyticus, confers resistance to β-lactam antibiotics through activating a β-lactamase gene. Its periplasmic sensor domain was p...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2020.107610
更新日期:2020-11-01 00:00:00
abstract::It has been postulated that phosphophoryn (PP) molecules bind specifically to type I collagen fibrils as the key event in inducing matrix mineralization in dentin. The nature and specificity of the collagen molecule-PP interaction has been examined by rotary shadowing-electron microscopy of mixtures of native, monomer...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1998.4025
更新日期:1998-10-01 00:00:00
abstract::The recent high-resolution structure of the toxin FraC derived from the sea anemone Actinia fragacea has provided new insight into the mechanism of pore formation by actinoporins. In this work, we report two new crystal forms of FraC in its oligomeric prepore conformation. Together with the previously reported structu...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2012.06.003
更新日期:2012-11-01 00:00:00
abstract::Two membrane-bound ATP-dependent AAA proteases conduct protein quality surveillance in the inner membrane of mitochondria and control crucial steps during mitochondrial biogenesis. AAA domains of proteolytic subunits are critical for the recognition of non-native membrane proteins which are extracted from the membrane...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2006.01.009
更新日期:2006-10-01 00:00:00
abstract::We have developed a simplified, efficient approach for the 3D reconstruction and analysis of mammalian cells in toto by electron microscope tomography (ET), to provide quantitative information regarding 'global' cellular organization at approximately 15-20 nm resolution. Two insulin-secreting beta cells-deemed 'functi...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2007.09.015
更新日期:2008-03-01 00:00:00
abstract::Aminoglycoside 4-phosphotransferase-Ia (APH(4)-Ia)/Hygromycin B phosphotransferase (Hph) inactivates the aminoglycoside antibiotic hygromycin B (hygB) via phosphorylation. The crystal structure of the binary complex of APH(4)-Ia with hygB was recently reported. To characterize substrate recognition by the enzyme, we d...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2013.05.023
更新日期:2013-07-01 00:00:00
abstract::The phycobilisome photosynthetic antenna complex, found in cyanobacteria and red-algae, interacts with proteins expressed specifically to deal with different forms of physiological stress. Under conditions of nutrient starvation, the NblA protein is required for the process that leads to phycobilisome degradation and ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2006.10.021
更新日期:2007-04-01 00:00:00
abstract::Neuropeptide gamma (NPgamma) is a neurokinin-2 (NK-2) receptor selective agonist, which plays an important role in mediation of asthma and elicits a wide range of biological responses like bronchoconstriction, vasodepression and regulation of endocrine functions. The structure determination of this peptide agonist is ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2004.08.008
更新日期:2004-12-01 00:00:00
abstract::The actin-like protein ParM forms the cytomotive filament of the ParMRC system, a type II plasmid segregation system encoded by Escherichia coli R1 plasmid. We report an 8.5Å resolution reconstruction of the ParM filament, obtained using cryo-electron microscopy. Fitting of the 3D density reconstruction with monomeric...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2013.02.010
更新日期:2013-10-01 00:00:00
abstract::We present RIBFIND, a method for detecting flexibility in protein structures via the clustering of secondary structural elements (SSEs) into rigid bodies. To test the usefulness of the method in refining atomic structures within cryoEM density we incorporated it into our flexible fitting protocol (Flex-EM). Our benchm...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.10.011
更新日期:2012-02-01 00:00:00
abstract::The goal of this study is to evaluate the performance of software for automated particle-boxing, and in particular the performance of a new tool (TextonSVM) that recognizes the characteristic texture of particles of interest. As part of a high-throughput protocol, we use human editing that is based solely on class-ave...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.05.017
更新日期:2011-09-01 00:00:00
abstract::Magnetotactic bacteria are Gram-negative bacteria that navigate along geomagnetic fields using the magnetosome, an organelle that consists of a membrane-enveloped magnetic nanoparticle. Magnetite formation and its properties are controlled by a specific set of proteins. MamC is a small magnetosome-membrane protein tha...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2016.03.001
更新日期:2016-06-01 00:00:00
abstract::Substrate binding to enzymes often follows a precise order where catalysis is accomplished through programmed conformational changes. Short-chain dehydrogenase/reductase (SDR) enzymes follow sequential order 'bi-bi' reaction kinetics. The mechanistic study of a SDR homolog, reductase (R) domain, from multifunctional e...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2014.07.008
更新日期:2014-09-01 00:00:00
abstract::The Contrast Transfer Function (CTF) of an image, which modulates images taken from a Transmission Electron Microscope (TEM), is usually determined from the radial average of the power spectrum of the image (Frank, J., Three-dimensional Electron Microscopy of Macromolecular Assemblies, Oxford University Press, Oxford,...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2008.06.012
更新日期:2008-10-01 00:00:00
abstract::The structure of the smooth muscle contractile apparatus was studied using ultrarapid freezing followed by freeze substitution or by longitudinal freeze-fracture, deep-etch, and platinum-carbon replication. Freeze substitution minimises the detrimental effects of chemical fixation and freeze fracture eliminates them e...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1995.1009
更新日期:1995-03-01 00:00:00
abstract::A new scanning probe microscope, the photonic force microscope (PFM), based on optical tweezers and two-photon absorption processes for biological applications is described. Optical tweezers are used to trap a fluorescent latex bead with a diameter of 200 nm in an aqueous solution in all three dimensions. The fluoresc...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1997.3880
更新日期:1997-07-01 00:00:00
abstract::In bacteria, the two-component system (TCS) is the most prevalent for sensing and transducing the environmental signals into the cell. In Salmonella, the small basic protein PmrD is found to protect phospho-PmrA and prolong the expression of PmrA-activated genes. In contrast, Escherichia coli PmrD fails to protect pho...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2010.06.007
更新日期:2010-12-01 00:00:00
abstract::X-ray imaging offers a new 3-D view into cells. With its ability to penetrate whole hydrated cells it is ideally suited for pairing fluorescence light microscopy and nanoscale X-ray tomography. In this paper, we describe the X-ray optical set-up and the design of the cryo full-field transmission X-ray microscope (TXM)...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2011.12.023
更新日期:2012-02-01 00:00:00
abstract::Polyketides such as the clinically-valuable antibacterial agent mupirocin are constructed by architecturally-sophisticated assembly lines known as trans-acyltransferase polyketide synthases. Organelle-sized megacomplexes composed of several copies of trans-acyltransferase polyketide synthase assembly lines have been o...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2015.12.011
更新日期:2016-03-01 00:00:00
abstract::In arthropods the cuticle forms an exoskeleton with its physical and chemical properties adapted to functions of distinct skeletal elements. The cuticle of the partes incisivae (PI) in mandibles of terrestrial isopods is a composite of chitin-protein fibrils/fibres and minerals. It consists of an unmineralized tip, a ...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2015.03.007
更新日期:2015-05-01 00:00:00
abstract::Anti-TRAP (AT) protein regulates expression of tryptophan biosynthetic genes by binding to the trp RNA-binding attenuation protein (TRAP) and preventing its interaction with RNA. Bacillus subtilis AT forms trimers that can either interact with TRAP or can further assemble into dodecameric particles. To determine which...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2010.01.013
更新日期:2010-04-01 00:00:00
abstract::Electron cryo-microscopy (cryo-EM) of purified macromolecular complexes is now providing 3D-structures at near-atomic resolution (Kühlbrandt, 2014). Cryo-EM can tolerate heterogeneous specimens, however, high-resolution efforts demand highly optimized samples. Therefore, significant pre-screening and evaluation is ess...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2018.05.008
更新日期:2018-09-01 00:00:00
abstract::The collagen which forms the egg case of the dogfish, Scyliorhinus canicula, is assembled in a three-dimensional network that results in a very resistant capsule. The capsule presumably accomplishes both a protective and a filtering role for the embryo contained within it. In the present work we have obtained electron...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1006/jsbi.1998.3994
更新日期:1998-01-01 00:00:00
abstract::Rlf is a guanine nucleotide exchange factor for the small G-proteins RalA and RalB and couples Ras- to Ral-signalling. Here the crystal structure of the catalytic module of Rlf consisting of a REM- and a CDC25-homology domain is determined. The structure is distinguished by an extended three stranded β-sheet called th...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2013.07.009
更新日期:2013-09-01 00:00:00
abstract::The aim of this work was to develop a protocol for automated tracking of actin filaments in electron tomograms of lamellipodia embedded in negative stain. We show that a localized version of the Radon transform for the detection of filament directions enables three-dimensional visualizations of filament network archit...
journal_title:Journal of structural biology
pub_type: 杂志文章
doi:10.1016/j.jsb.2012.02.011
更新日期:2012-04-01 00:00:00