Improved applicability and robustness of fast cryo-electron tomography data acquisition.

Abstract:

:The power of cryo-electron tomography (cryoET) lies in its capability to characterize macromolecules in their cellular context. Structure determination by cryoET, however, is time-consuming compared to single particle approaches. A recent study reported significant acceleration of data acquisition by a fast-incremental single-exposure (FISE) tilt series scheme. Here we improved the method and evaluated its efficiency and performance. We show that (1) FISE combined with the latest generation of direct electron detectors speeds up collection considerably, (2) previous generation (pre-2017) double-tilt axis Titan Krios holders are also suitable for FISE data acquisition, (3) x, y and z-specimen shifts can be compensated for, and (4) FISE tilt series data can generate averages of sub-nanometer resolution. These advances will allow for a widespread adoption of cryoET for high-throughput in situ studies and high-resolution structure determination across different biological research disciplines.

journal_name

J Struct Biol

authors

Eisenstein F,Danev R,Pilhofer M

doi

10.1016/j.jsb.2019.08.006

subject

Has Abstract

pub_date

2019-11-01 00:00:00

pages

107-114

issue

2

eissn

1047-8477

issn

1095-8657

pii

S1047-8477(19)30176-5

journal_volume

208

pub_type

杂志文章
  • Maximum likelihood refinement of electron microscopy data with normalization errors.

    abstract::Commonly employed data models for maximum likelihood refinement of electron microscopy images behave poorly in the presence of normalization errors. Small variations in background mean or signal brightness are relatively common in cryo-electron microscopy data, and varying signal-to-noise ratios or artifacts in the im...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2009.02.007

    authors: Scheres SH,Valle M,Grob P,Nogales E,Carazo JM

    更新日期:2009-05-01 00:00:00

  • Delineating the reaction mechanism of reductase domains of Nonribosomal Peptide Synthetases from mycobacteria.

    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

    authors: Haque AS,Patel KD,Deshmukh MV,Chhabra A,Gokhale RS,Sankaranarayanan R

    更新日期:2014-09-01 00:00:00

  • Importance of detergent and phospholipid in the crystallization of the human erythrocyte anion-exchanger membrane domain.

    abstract::Three-dimensional crystals were obtained for the membrane domain of the human erythrocyte anion exchanger (AE1, Band 3). Protein homogeneity and stability and the delicate balance between the detergent used and the amount of phospholipids copurifying are critical to the formation of three-dimensional crystals of the A...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/s1047-8477(02)00010-2

    authors: Lemieux MJ,Reithmeier RA,Wang DN

    更新日期:2002-03-01 00:00:00

  • Unsupervised mitochondria segmentation using recursive spectral clustering and adaptive similarity models.

    abstract::The unsupervised segmentation method proposed in the current study follows the evolutional ability of human vision to extrapolate significant structures in an image. In this work we adopt the perceptual grouping strategy by selecting the spectral clustering framework, which is known to capture perceptual organization ...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2013.10.013

    authors: Dietlmeier J,Ghita O,Duessmann H,Prehn JH,Whelan PF

    更新日期:2013-12-01 00:00:00

  • IRIS explorer software for radial-depth cueing reovirus particles and other macromolecular structures determined by cryoelectron microscopy and image reconstruction.

    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

    authors: Spencer SM,Sgro JY,Dryden KA,Baker TS,Nibert ML

    更新日期:1997-10-01 00:00:00

  • Finding rigid bodies in protein structures: Application to flexible fitting into cryoEM maps.

    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

    authors: Pandurangan AP,Topf M

    更新日期:2012-02-01 00:00:00

  • Tomo3D 2.0--exploitation of advanced vector extensions (AVX) for 3D reconstruction.

    abstract::Tomo3D is a program for fast tomographic reconstruction on multicore computers. Its high speed stems from code optimization, vectorization with Streaming SIMD Extensions (SSE), multithreading and optimization of disk access. Recently, Advanced Vector eXtensions (AVX) have been introduced in the x86 processor architect...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2014.11.009

    authors: Agulleiro JI,Fernandez JJ

    更新日期:2015-02-01 00:00:00

  • Interdoublet sliding in bovine spermatozoa: its relationship to flagellar motility and the action of inhibitory agents.

    abstract::Interdoublet sliding rates were assessed in bull sperm, utilizing a freeze-thaw procedure to allow axonemal disintegration. The sliding rate of 23 degrees C increased with increasing MgATP concentrations up to 1 mM ATP, to plateau at 8 microns/sec. The analyzed interdoublet shear in both live and demembranated (Triton...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1006/jsbi.1996.0059

    authors: Bird Z,Hard R,Kanous KS,Lindemann CB

    更新日期:1996-05-01 00:00:00

  • Zernike phase contrast cryo-electron tomography of sodium-driven flagellar hook-basal bodies from Vibrio alginolyticus.

    abstract::Vibrio alginolyticus use flagella to swim. A flagellum consists of a filament, hook and basal body. The basal body is made up of a rod and several ring structures. This study investigates the structure of the T ring which is a unique component of the V. alginolyticus sodium ion-driven flagellar basal body. Using Zerni...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2010.08.004

    authors: Hosogi N,Shigematsu H,Terashima H,Homma M,Nagayama K

    更新日期:2011-01-01 00:00:00

  • Investigation of the human pineal gland 3D organization by X-ray phase contrast tomography.

    abstract::Pineal gland (PG) is a part of the human brain epithalamus that plays an important role in sleep, circadian rhythm, immunity, and reproduction. The calcium deposits and lesions in PG interfere with normal function of the organ and can be associated with different health disorders including serious neurological disease...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2020.107659

    authors: Bukreeva I,Junemann O,Cedola A,Palermo F,Maugeri L,Begani Provinciali G,Pieroni N,Sanna A,Otlyga DA,Buzmakov A,Krivonosov Y,Zolotov D,Chukalina M,Ivanova A,Saveliev S,Asadchikov V,Fratini M

    更新日期:2020-12-01 00:00:00

  • The fibrils of Ure2p homologs from Saccharomyces cerevisiae and Saccharoymyces paradoxus have similar cross-β structure in both dried and hydrated forms.

    abstract::The ability to convert into amyloid fibrils is a common feature of prion proteins. However, not all amyloid-forming proteins act as prions. Here, we compared two homologs of the yeast prion protein Ure2 from Saccharomyces cerevisiae and Saccharomyces paradoxus, ScUre2p and SpUre2p, which have different prion propensit...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2011.03.008

    authors: Wang YQ,Bongiovanni M,Gras SL,Perrett S

    更新日期:2011-06-01 00:00:00

  • Seeds to crystals.

    abstract::Seeding has been critical for obtaining diffraction-quality crystals for many structures. In this article, applications and recommendations for seeding are presented based on examples from our laboratory and other groups. The implementation of seeding in high-throughput crystallization, robotics, and other emerging te...

    journal_title:Journal of structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/s1047-8477(03)00039-x

    authors: Bergfors T

    更新日期:2003-04-01 00:00:00

  • Mollicutes-wall-less bacteria with internal cytoskeletons.

    abstract::The structure and motility of the Mollicutes (Spiroplasma, Mycoplasma, and Acholeplasma) are briefly reviewed. The data are presented from the perspective of prokaryotic and eukaryotic motors, cytoskeletons, and cell motility. The Mollicutes are eubacteria derived from Clostridia by regressive evolution and genome red...

    journal_title:Journal of structural biology

    pub_type: 杂志文章,评审

    doi:10.1006/jsbi.1998.4063

    authors: Trachtenberg S

    更新日期:1998-12-15 00:00:00

  • Ultrastructural changes in the retinopathy, globe enlarged (rge) chick cornea.

    abstract::In the cornea, the precise organisation of fibrillar collagen and associated proteoglycans comprising the stromal extracellular matrix plays a major role in governing tissue form and function. Recently, abnormal collagen alignment was noted in the misshapen corneas of mature chickens affected by the retinopathy, globe...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2009.01.009

    authors: Boote C,Hayes S,Young RD,Kamma-Lorger CS,Hocking PM,Elsheikh A,Inglehearn CF,Ali M,Meek KM

    更新日期:2009-05-01 00:00:00

  • Conical Fourier shell correlation applied to electron tomograms.

    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

    authors: Diebolder CA,Faas FG,Koster AJ,Koning RI

    更新日期:2015-05-01 00:00:00

  • Insights into the composition, morphology, and formation of the calcareous shell of the serpulid Hydroides dianthus.

    abstract::To date, the calcareous tubes of serpulid marine worms have not been studied extensively in a biomineralization context. The structure and composition of the tube shell and adhesive cement of the marine tubeworm Hydroides dianthus were studied using a variety of characterization techniques, including powder XRD, FTIR,...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2009.09.008

    authors: Tanur AE,Gunari N,Sullan RM,Kavanagh CJ,Walker GC

    更新日期:2010-02-01 00:00:00

  • Crystallization of sparingly soluble stress-related proteins from cyanobacteria by controlled urea solublization.

    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

    authors: Dines M,Sendersky E,Schwarz R,Adir N

    更新日期:2007-04-01 00:00:00

  • Tooth movements are guided by specific contact areas between the tooth root and the jaw bone: A dynamic 3D microCT study of the rat molar.

    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

    authors: Naveh GR,Shahar R,Brumfeld V,Weiner S

    更新日期:2012-02-01 00:00:00

  • Dry and survive: morphological changes during anhydrobiosis in a bdelloid rotifer.

    abstract::Bdelloid rotifers are aquatic microinvertebrates able to cope with the loss of environmental water by entering dormancy, and are thus capable of living in temporary habitats. When water is evaporating, bdelloids contract into "tuns", silence metabolism and lose water from the body, a condition known as anhydrobiosis. ...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2010.04.003

    authors: Marotta R,Leasi F,Uggetti A,Ricci C,Melone G

    更新日期:2010-07-01 00:00:00

  • The three-dimensional structure of trypsin-treated Staphylococcus aureus alpha-toxin.

    abstract::Trypsin treatment of staphylococcal alpha-toxin cleaves the molecule into two roughly equally sized parts, which results in inactivation of the toxin. Tetragonal arrays of oligomers, closely resembling the native ones, can however be formed on lipid layers. From tilted views of negatively stained crystals a 3D structu...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/1047-8477(92)90024-5

    authors: Olofsson A,Kavéus U,Thelestam M,Hebert H

    更新日期:1992-05-01 00:00:00

  • Substrate specific consequences of central pore mutations in the i-AAA protease Yme1 on substrate engagement.

    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

    authors: Graef M,Langer T

    更新日期:2006-10-01 00:00:00

  • Three-dimensional reconstruction of collagen-proteoglycan interactions in the mouse corneal stroma by electron tomography.

    abstract::Corneal transparency is fundamental to the visual system, and is directly related to the ordered collagen fibril architecture that the cornea maintains. Proteoglycans, through their protein core and highly anionic glycosaminoglycan side chains, are thought to regulate the collagen organisation in the corneal stroma. T...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2010.01.019

    authors: Parfitt GJ,Pinali C,Young RD,Quantock AJ,Knupp C

    更新日期:2010-05-01 00:00:00

  • Repetitive versus monomeric antigen presentation: direct visualization of antibody affinity and specificity.

    abstract::The concept of presenting antigens in a repetitive array to obtain high titers of specific antibodies is increasingly applied by using surface-engineered viruses or bacterial envelopes as novel vaccines. A case for this concept was made 25 years ago, when producing high-titer antisera against ordered arrays of gp23, t...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2003.08.004

    authors: Baschong W,Hasler L,Häner M,Kistler J,Aebi U

    更新日期:2003-09-01 00:00:00

  • Structural basis for pH dependent monomer-dimer transition of 3,4-dihydroxy 2-butanone-4-phosphate synthase domain from Mycobacterium tuberculosis.

    abstract::3,4-dihydroxy 2-butanone 4-phosphate synthase (DHBPS) and GTP cyclohydrolase-II (GTPCH-II) are the two initial enzymes involved in riboflavin biosynthesis pathway, which has been shown to be essential for the pathogens. In Mycobacterium tuberculosis (Mtb), the ribA2 gene (Rv1415) encodes for the bi-functional enzyme w...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2011.01.013

    authors: Singh M,Kumar P,Karthikeyan S

    更新日期:2011-05-01 00:00:00

  • Accurate modeling of single-particle cryo-EM images quantitates the benefits expected from using Zernike phase contrast.

    abstract::The use of a Zernike-type phase plate in biologic cryo-electron microscopy allows the imaging, without using defocus, of what are predominantly phase objects. It is thought that such phase-plate implementations might result in higher quality images, free from the problems of CTF correction that occur when images must ...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2011.03.020

    authors: Hall RJ,Nogales E,Glaeser RM

    更新日期:2011-06-01 00:00:00

  • Conformational plasticity of the response regulator CpxR, a key player in Gammaproteobacteria virulence and drug-resistance.

    abstract::The transcriptional regulator CpxR mediates an adaptive response to envelope stress, tightly linked to virulence and antibiotics resistance in several Gammaproteobacteria pathogens. In this work, we integrated crystallographic and small-angle X-ray scattering data to gain insights into the structure and conformational...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2018.08.001

    authors: Mechaly AE,Haouz A,Sassoon N,Buschiazzo A,Betton JM,Alzari PM

    更新日期:2018-11-01 00:00:00

  • A first census of collagen interruptions: collagen's own stutters and stammers.

    abstract::The repetitive Gly-X-Y sequence is the telltale sign of triple helical domains in collagens and collagen-like proteins. Most collagen sequences contain sporadic interruptions of this pattern, which may have functional roles in molecular flexibility, assembly or molecular recognition. However, the structural signatures...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2014.03.022

    authors: Bella J

    更新日期:2014-06-01 00:00:00

  • Single versus dual-axis cryo-electron tomography of microtubules assembled in vitro: limits and perspectives.

    abstract::Single-axis cryo-electron tomography of vitrified specimens has become a method of choice to reconstruct in three dimensions macromolecular assemblies in their cellular context or prepared from purified components. Here, we asked how a dual-axis acquisition scheme would improve three-dimensional reconstructions of mic...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2012.11.004

    authors: Guesdon A,Blestel S,Kervrann C,Chrétien D

    更新日期:2013-02-01 00:00:00

  • High-resolution structures of annexin A5 in a two-dimensional array.

    abstract::Annexins are soluble cytosolic proteins that bind to cell membranes. Annexin A5 self-assembles into a two-dimensional (2D) array and prevents cell rupture by attaching to damaged membranes. However, this process is not fully understood at the molecular level. In this study, we determined the crystal structures of anne...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2019.10.003

    authors: Hong S,Na S,Kim OH,Jeong S,Oh BC,Ha NC

    更新日期:2020-01-01 00:00:00

  • Applications of the molecular dynamics flexible fitting method.

    abstract::In recent years, cryo-electron microscopy (cryo-EM) has established itself as a key method in structural biology, permitting the structural characterization of large biomolecular complexes in various functional states. The data obtained through single-particle cryo-EM has recently seen a leap in resolution thanks to l...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2010.09.024

    authors: Trabuco LG,Schreiner E,Gumbart J,Hsin J,Villa E,Schulten K

    更新日期:2011-03-01 00:00:00