Abstract：
:As a long-term goal we want to use cryoelectron tomography to understand how non-enveloped viruses, such as picornaviruses, enter cells and translocate their genomes across membranes. To this end, we developed new image-processing tools using an in vitro system to model viral interactions with membranes. The complex of poliovirus with its membrane-bound receptors was reconstructed by averaging multiple sub-tomograms, thereby producing three-dimensional maps of surprisingly high-resolution (30 A). Recognizable images of the complex could be produced by averaging as few as 20 copies. Additionally, model-free reconstructions of free poliovirus particles, clearly showing the major surface features, could be calculated from 60 virions. All calculations were designed to avoid artifacts caused by missing information typical for tomographic data ("missing wedge"). To investigate structural and conformational variability we applied a principal component analysis classification to specific regions. We show that the missing wedge causes a bias in classification, and that this bias can be minimized by supplementation with data from the Fourier transform of the averaged structure. After classifying images of the receptor into groups with high similarity, we were able to see differences in receptor density consistent with the known variability in receptor glycosylation.
journal_name
J Struct Bioljournal_title
Journal of structural biologyauthors
Bostina M,Bubeck D,Schwartz C,Nicastro D,Filman DJ,Hogle JMdoi
10.1016/j.jsb.2007.08.009subject
Has Abstractpub_date
2007-11-01 00:00:00pages
200-10issue
2eissn
1047-8477issn
1095-8657pii
S1047-8477(07)00196-7journal_volume
160pub_type
杂志文章abstract：:Macromolecular complexes perform their physiological functions by local rearrangements of their constituents and biochemically interacting with their reaction partners. These rearrangements may involve local rotations and the induction of local strains causing different mechanical efforts and stretches at the differen...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2016.04.001
更新日期：2016-07-01 00:00:00
abstract：:Hard X-ray fluorescence microscopy and magnified phase contrast imaging are combined to obtain quantitative maps of the projected metal concentration in whole cells. The experiments were performed on freeze dried cells at the nano-imaging station ID22NI of the European Synchrotron Radiation Facility (ESRF). X-ray fluo...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.12.005
更新日期：2012-02-01 00:00:00
abstract：:The protist Trypanosoma brucei is an emerging model for the study of cilia and flagella. Here, we used scanning transmission electron microscopy (STEM) tomography to describe the structure of the trypanosome transition zone (TZ). At the base of the TZ, nine transition fibres irradiate from the B microtubule of each do...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2017.12.005
更新日期：2018-04-01 00:00:00
abstract：:Traditional single particle reconstruction methods use either the Fourier or the delta function basis to represent the particle density map. This paper proposes a more flexible algorithm that adaptively chooses the basis based on the data. Because the basis adapts to the data, the reconstruction resolution and signal-...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2012.04.012
更新日期：2012-07-01 00:00:00
abstract：:The resolution of electron tomograms is anisotropic due to geometrical constraints during data collection, such as the limited tilt range and single axis tilt series acquisition. Acquisition of dual axis tilt series can decrease these effects. However, in cryo-electron tomography, to limit the electron radiation damag...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2015.03.010
更新日期：2015-05-01 00:00:00
abstract：:Chaperonins mediate protein folding in an ATP-dependent manner. ATP binding and hydrolysis by chaperonins are subject to both homotropic and heterotropic allosteric regulation. In the case of GroEL and CCT, homotropic regulation by ATP is manifested in nested cooperativity, which involves positive intra-ring cooperati...
journal_title：Journal of structural biology
pub_type： 杂志文章,评审
doi：10.1006/jsbi.2001.4377
更新日期：2001-08-01 00:00:00
abstract：:A new era has begun for single particle cryo-electron microscopy (cryoEM) which can now compete with X-ray crystallography for determination of protein structures. The development of direct detectors constitutes a revolution that has led to a wave of near-atomic resolution cryoEM reconstructions. However, regardless o...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2014.09.008
更新日期：2014-11-01 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：:A topological localization of epitopes on the surface of the Aa6 subunit of Androctonus australis hemocyanin has been carried out. First, immunocomplex strings composed of native hemocyanin and monoclonal antibodies were examined in the electron microscope and submitted to an image processing by correspondence analysi...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(90)90087-s
更新日期：1990-03-01 00:00:00
abstract：:When biological macromolecules are imaged in the transmission electron microscope (TEM), their inherent handedness is lost because the three-dimensional (3D) structure is projected onto a two-dimensional (2D) plane, and identical 2D projections can be made from either 3D enantiomer. Nevertheless, tilt experiments in t...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1997.3896
更新日期：1997-10-01 00:00:00
abstract：:Structures of biological macromolecules determined by transmission cryoelectron microscopy (cryo-TEM) and three-dimensional image reconstruction are often displayed as surface-shaded representations with depth cueing along the viewed direction (Z cueing). Depth cueing to indicate distance from the center of virus part...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1997.3902
更新日期：1997-10-01 00:00:00
abstract：:Hypercalcified sponges, endowed with a calcium carbonate basal skeleton in addition to their spicules, form one of the most basal metazoan group engaged in extensive biomineralization. The Mediterranean species Petrobiona massiliana was used to investigate biological controls exerted on the biomineralization of its ba...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2012.04.004
更新日期：2012-06-01 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：:Enameloid, the hyper-mineralized tissue covering shark teeth is a complex structure resulting from both ameloblast and odontoblast activity. The way these two types of cells interact to set up this tissue is not fully understood and results in the formation of subunits in the enameloid: the Single Crystallite Enameloi...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2020.107664
更新日期：2020-11-19 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
abstract：:In order to understand further the mechanism of bone fracture repair, and thus to innovate better operative treatment for bone fracture and to design new implant materials for bone repair, microstructures of external periosteal callus (EPC) of repaired femoral fracture in both children and adults were investigated by ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1996.0084
更新日期：1996-11-01 00:00:00
abstract：:Ferritin, the major iron storage protein, has dual functions; it sequesters redox activity of intracellular iron and facilitates iron turn-over. Here we present high angle annular dark field (HAADF) images from individual hepatic ferritin cores within tissue sections, these images were obtained using spherical aberrat...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2008.12.001
更新日期：2009-04-01 00:00:00
abstract：:The structure of Panicum Mosaic Virus (PMV) was determined by X-ray diffraction analysis to 2.9Å resolution. The crystals were of pseudo symmetry F23; the true crystallographic unit cell was of space group P2(1) with a=411.7Å, b=403.9Å and c=412.5Å, with β=89.7°. The asymmetric unit was two entire T=3 virus particles,...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2012.10.012
更新日期：2013-01-01 00:00:00
abstract：:In order to successfully perform the 3D reconstruction in electron tomography, transmission electron microscope images must be accurately aligned or registered. So far, the problem is solved by either manually showing the corresponding fiducial markers from the set of images or automatically using simple correlation b...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.2001.4343
更新日期：2001-01-01 00:00:00
abstract：:This study demonstrates the effects of progesterone on eggshell quality and ultrastructure by injecting progesterone into laying hens 2 and 5 h post-oviposition, respectively. Progesterone injected 2 h post-oviposition (P4-2 h) improved eggshell quality with a significant decrease (P < 0.01) in the thickness of the ma...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2019.107430
更新日期：2020-02-01 00:00:00
abstract：:Three questions central to understanding the initiation of DNA replication in eukaryotes are: (1) Does DNA synthesis begin at a defined place? (2) What determines replication initiation sites? (3) What regulates an origin to fire only once per cell cycle? A key player in this is the origin recognition complex (ORC), r...
journal_title：Journal of structural biology
pub_type： 杂志文章,评审
doi：10.1016/s1047-8477(02)00538-5
更新日期：2002-10-01 00:00:00
abstract：:A comprehensive analysis of the sequences of all types of intermediate filament chains has been undertaken with a particular emphasis on those of segment 1A and linker L1. This has been done to assess whether structural characteristics can be recognized in the sequences that would be consistent with the role of each r...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.2002.4438
更新日期：2002-01-01 00:00:00
abstract：:We have previously used cryo-electron tomography combined with sub-volume averaging and classification to obtain 3D structures of macromolecular assemblies in cases where a single dominant species was present, and applied these methods to the analysis of a variety of trimeric HIV-1 and SIV envelope glycoproteins (Env)...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2012.01.004
更新日期：2012-05-01 00:00:00
abstract：:The ultrastructure of β-chitin microfibrils from a centric diatom, Thalassiosira, and a tubeworm, Lamellibrachia, was studied using electron diffraction and high-resolution electron microscopy. Electron microdiffraction diagrams corresponding to each projection of the β-chitin crystals were obtained, and all the data ...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2011.07.001
更新日期：2011-10-01 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：:Formation of filaments by the Ure2 protein constitutes the molecular mechanism of the [URE3] prion in yeast. According to the "amyloid backbone" model, the N-terminal asparagine-rich domains of Ure2p polymerize to form an amyloid core fibril that is surrounded by C-terminal domains in their native conformation. Protea...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2005.02.007
更新日期：2005-05-01 00:00:00
abstract：:The cyclooxygenases (COX-1 and COX-2) catalyze the rate-limiting step in the biosynthesis of prostaglandins, and are the pharmacological targets of non-steroidal anti-inflammatory drugs (NSAIDs) and COX-2 selective inhibitors (coxibs). Ibuprofen (IBP) is one of the most commonly available over-the-counter pharmaceutic...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2014.11.005
更新日期：2015-01-01 00:00:00
abstract：:We report a detailed work of composition and location of naturally formed iron biominerals in plant cells tissues grown in iron rich environments as Imperata cylindrica. This perennial grass grows on the Tinto River banks (Iberian Pyritic Belt) in an extreme acidic ecosystem (pH∼2.3) with high concentration of dissolv...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/j.jsb.2015.11.005
更新日期：2016-01-01 00:00:00
abstract：:Different types of cells have been imaged with the atomic force microscope. The morphology of the archaebacterium Halobacterium halobium in its dry state was revealed. On a leaf of the small Indian tree Lagerstroemia subcostata a stoma was imaged. The lower side of a water lily leaf was imaged in water showing feature...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1016/1047-8477(90)90098-w
更新日期：1990-10-01 00:00:00
abstract：:Calnexin is a molecular chaperone that facilitates folding of glycoproteins in the endoplasmic reticulum (ER). The cloned lumenal domain of canine calnexin, cnxDeltaTMC, retains its biological activity without the transmembrane and cytosolic region. For the purpose of structure determination we generated a crystalliza...
journal_title：Journal of structural biology
pub_type： 杂志文章
doi：10.1006/jsbi.1998.4032
更新日期：1998-11-01 00:00:00
