Abstract：
:CTFFIND is a widely-used program for the estimation of objective lens defocus parameters from transmission electron micrographs. Defocus parameters are estimated by fitting a model of the microscope's contrast transfer function (CTF) to an image's amplitude spectrum. Here we describe modifications to the algorithm which make it significantly faster and more suitable for use with images collected using modern technologies such as dose fractionation and phase plates. We show that this new version preserves the accuracy of the original algorithm while allowing for higher throughput. We also describe a measure of the quality of the fit as a function of spatial frequency and suggest this can be used to define the highest resolution at which CTF oscillations were successfully modeled.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Rohou A,Grigorieff Ndoi
10.1016/j.jsb.2015.08.008subject
Has Abstractpub_date
2015-11-01 00:00:00pages
216-21issue
2eissn
1047-8477issn
1095-8657pii
S1047-8477(15)30046-0journal_volume
192pub_type
杂志文章abstract：:Folding and self-assembly of amyloid beta (Abeta) peptide are linked to Alzheimer's disease. To understand the initial stage of amyloid-beta peptide aggregation, conformational characteristics of monomers of wild-type (WT) Abeta(28-35) and its mutant peptides A30G and A30I were investigated using density functional th...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2010.02.017
更新日期：2010-06-01 00:00:00
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 particl...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1998.4011
更新日期：1998-09-01 00:00:00
abstract：:Tobacco mosaic virus (TMV) is a plant virus with a highly ordered organisation and has been described in three different structural states: As stacked disks without RNA (X-ray crystallography), as a helical form with RNA (X-ray fibre diffraction) and as a second distinct helical form with RNA (cryo-EM). Here we presen...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2010.06.011
更新日期：2010-09-01 00:00:00
abstract：:Hedgehog signaling plays a crucial role in embryogenesis and adult tissue homeostasis, and mutations of its key components such as Suppressor of fused (Sufu) are closely associated with human diseases. The Ser/Thr kinase Fused (Fu) promotes Hedgehog signaling by phosphorylating the Cubitus interruptus (Ci)/Glioma-asso...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2020.107614
更新日期：2020-11-01 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：:Electron cryo-tomography (cryoET) is currently the only technique that allows the direct observation of proteins in their native cellular environment. Sub-volume averaging of electron tomograms offers a route to increase the signal-to-noise of repetitive biological structures, such improving the information content an...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2016.06.024
更新日期：2017-02-01 00:00:00
abstract：:Since the foundation for the three-dimensional image reconstruction of helical objects from electron micrographs was laid more than 30 years ago, there have been sustained developments in specimen preparation, data acquisition, image analysis, and interpretation of results. However, the boxing of filaments in large nu...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.2001.4415
更新日期：2001-09-01 00:00:00
abstract：:We present a strategy to obtain milligrams of highly post-translationally modified eukaryotic proteins, transiently expressed in mammalian cells as rigid or cleavable fusions with a mammalianized version of bacterial maltose-binding protein (mMBP). This variant was engineered to combine mutations that enhance MBP solu...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2016.01.016
更新日期：2016-04-01 00:00:00
abstract：:Polynoid worm elytra emit light when mechanically or electrically stimulated. Specialized cells, the photocytes, contain light emitting machineries, the photosomes. Successive stimulations induce light intensity variations and show a coupling within and between photosomes. Here, we describe, using electron tomography ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2017.12.001
更新日期：2018-04-01 00:00:00
abstract：:We describe novel structural domains in in vitro reconstituted Xenopus sperm nuclei, which we term RPA bodies; RPA is the only known marker of these structures. These bodies contain DNA and represent special chromatin domains as seen by transmission electron microscopy. We show that RPA bodies exhibit a similar ultras...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.2000.4229
更新日期：2000-04-01 00:00:00
abstract：:The yeast peroxisomal hydrolase Lpx1 belongs to the α/β-hydrolase superfamily. In the absence of Lpx1, yeast peroxisomes show an aberrant vacuolated morphology similar to what is found in peroxisomal disorder patients. Here, we present the crystal structure of Lpx1 determined at a resolution of 1.9 Å. The structure re...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.06.008
更新日期：2011-09-01 00:00:00
abstract：:Like in most Crustacea, the cuticle of terrestrial isopods is hardened by a calcareous mineral phase. This rigid cuticle is frequently shed during a process called moulting. To reduce calcium loss, Porcellio scaber eats the shed cuticle, the exuviae, and absorb the calcium from it through large tubular diverticula of ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2020.107613
更新日期：2020-11-01 00:00:00
abstract：:Control of tissue composition and organization will be a key feature in the development of successful products through tissue engineering. However, the mechanism of collagen fibril formation, growth, and organization is not yet fully understood. In this study we have examined collagen fibril formation in a wound heali...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.2002.4460
更新日期：2002-01-01 00:00:00
abstract：:A simple, fast and efficient noise-reduction protocol for three-dimensional electron tomographic reconstructions of biological material is presented. The approach is based on iterative application of median filtering and shows promise for automatic noise reduction as a pre-processor for automated data analysis tools w...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2006.10.030
更新日期：2007-05-01 00:00:00
abstract：:The analysis of structure factors in 3D cryo-EM Coulomb potential maps and their "enhancement" at the end of the reconstruction process is a well-established practice, normally referred to as sharpening. The aim is to increase contrast and, in this way, to help tracing the atomic model. The most common way to accompli...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2020.107447
更新日期：2020-03-01 00:00:00
abstract：:The epithelial cell lining of the respiratory groove of Alma emini, an oligochaete glossoscolecid worm that lives in a hydrogen sulfide (H2S)-rich tropical swamp, was investigated by transmission electron microscopy to determine the underlying structural adaptations which enable the worm to subsist in a highly inimica...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1998.4000
更新日期：1998-01-01 00:00:00
abstract：:The question as to whether keratin intermediate filaments (KIF) are built from a unique "building block" consisting of a pair of coiled-coil molecules has been studied by examining the earliest stages of reassembly of mouse K1/K10 KIF in vitro. Particles formed in protein solutions of about 45 micrograms/ml (near or b...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(91)90020-w
更新日期：1991-10-01 00:00:00
abstract：:Amelogenin is believed to be involved in controlling the formation of the highly anisotropic and ordered hydroxyapatite crystallites that form enamel. The adsorption behavior of amelogenin proteins onto substrates is very important because protein-surface interactions are critical to its function. We have previously u...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2009.10.007
更新日期：2010-03-01 00:00:00
abstract：:A Gatan 1024 x 1024 slow-scan charge-coupled device (CCD) camera has been interfaced to a JEOL4000EX electron cryomicroscope and explored for its usefulness in the electron crystallographic analysis of thin, glucose-embedded crystals of crotoxin complex kept at -125 degrees C. We show that the camera allows for an on-...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1994.1029
更新日期：1994-07-01 00:00:00
abstract：:A common technique in transmission electron microscopy is the collection of a focal pair, in which the first, close to focus image contains higher resolution information at lower contrast, and the second, far from focus image has high contrast but less reliable high-resolution information. Typically these second micro...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2003.10.012
更新日期：2003-10-01 00:00:00
abstract：:Teeth sustain high loads over a lifetime and yet intact tooth failure is rare. The different structures of the tooth, jaw bone and the intervening soft periodontal ligament enable the tooth to endure repeated loading during mastication. Although mechanical and functional properties of the different components are thor...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.11.019
更新日期：2012-02-01 00:00:00
abstract：:Hyaline cartilage consists of sparse chondrocytes and abundant extracellular matrix. There is a paucity of experimental data in support of the notion of conceivable regional differences in the mechanical properties of chondral matrices. Upon visual differentiation of the pericellular and interterritorial matrices in e...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2003.10.003
更新日期：2004-03-01 00:00:00
abstract：:We have developed a new two-step algorithm to determine the astigmatism of images from transmission electron microscopes (TEMs). Instead of computing the radial average of the power spectrum, we divide the power spectrum of a TEM image 1 to m (typically 32) sectors. We use a technique based on perturbation analysis of...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2006.07.021
更新日期：2007-01-01 00:00:00
abstract：:A method based on Fourier transforms is described for obtaining a 3-D reconstruction from a paracrystalline object with static disorder. The method is derived from the standard methods used in 3-D reconstruction of 2-D crystals except that all of the Fourier coefficients are used and not just the sampled data from the...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1997.3932
更新日期：1997-12-01 00:00:00
abstract：:Random spherically constrained (RSC) single particle reconstruction is a method to obtain structures of membrane proteins embedded in lipid vesicles (liposomes). As in all single-particle cryo-EM methods, structure determination is greatly aided by reliable detection of protein "particles" in micrographs. After fittin...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2014.01.004
更新日期：2014-03-01 00:00:00
abstract：:The human vertebral body and intervertebral disc interface forms the region where the cartilaginous endplate, annulus fibrosis and bone of the vertebral body are connected through an intermediate calcified cartilage layer. While properties of both the vertebral body and components of the disc have been extensively stu...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2013.08.011
更新日期：2013-11-01 00:00:00
abstract：:In cryo-electron microscopy (cryo-EM) single-particle reconstruction, the heterogeneity of two-dimensional projection image data resulting from the co-existence of different conformational or ligand binding states of a macromolecular complex remains a major obstacle as it impairs the validity of reconstructed density ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2006.06.012
更新日期：2007-01-01 00:00:00
abstract：:Three-dimensional reconstruction of large macromolecules like viruses at resolutions below 10 A requires a large set of projection images. Several automatic and semi-automatic particle detection algorithms have been developed along the years. Here we present a general technique designed to automatically identify the p...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2003.11.028
更新日期：2004-01-01 00:00:00
abstract：:The cartilage is composed of chondrocytes embedded in a matrix of collagen fibrils interspersed within a network of proteoglycans and is constantly exposed to biomechanical forces during normal joint movement. Characterization of the surface morphology, cytoskeletal structure, adherance and elastic properties of these...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2008.02.005
更新日期：2008-06-01 00:00:00
abstract：:Titin is a giant protein that spans half of the striated muscle sarcomere. The I-band portion of titin extends as the sarcomere is stretched, developing what is known as passive force. This portion of the molecule is composed mainly of tandem immunoglobulin (Ig) segments, consisting of serially linked Ig-like domains,...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1998.3984
更新日期：1998-01-01 00:00:00
