Use of frozen-hydrated axonemes to assess imaging parameters and resolution limits in cryoelectron tomography.

Abstract:

:Using a 400-kV cryoelectron microscope, we have obtained tomographic reconstructions of frozen-hydrated sea urchin axonemes with 8-10-nm resolution, as assessed by detection of characteristic components including doublet microtubules, radial spokes, central sheath projections, and outer dynein arms. We did not detect the inner dynein arms or the microtubule lattice. The 1/(8 nm) and 1/(16 nm) layer lines are consistently present in power spectra of both projection images and tomographic reconstructions. Strength and detection of the layer lines are dependent upon total electron dose and defocus. Both layer lines are surprisingly resistant to electron doses of up to 11000 electrons/nm(2). We present a summary of resolution considerations in cryoelectron tomography and conclude that the fundamental limitation is the total electron dose required for statistical significance. The electron dose can be fractionated among the numerous angular views in a tomographic data set, but there is an unavoidable fourth-power dependence of total dose on target resolution. Since higher-resolution features are more beam-sensitive, this dose requirement places an ultimate limit on the resolution of individual tomographic reconstructions. Instrumental and computational strategies to circumvent this limitation are discussed.

journal_name

J Struct Biol

authors

McEwen BF,Marko M,Hsieh CE,Mannella C

doi

10.1016/s1047-8477(02)00020-5

keywords:

subject

Has Abstract

pub_date

2002-04-01 00:00:00

pages

47-57

issue

1-2

eissn

1047-8477

issn

1095-8657

pii

S1047847702000205

journal_volume

138

pub_type

杂志文章
  • De novo design of a two-stranded coiled-coil switch peptide.

    abstract::The properties and characteristics shared by amyloid fibrils formed from disease and non-disease associated proteins that are unrelated in sequence and structure offer the prospect that model systems can be used to systematically assess the factors that predispose a native protein to form amyloid fibrils. Based on a d...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2006.01.017

    authors: Kammerer RA,Steinmetz MO

    更新日期:2006-08-01 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

  • Improving coiled coil stability while maintaining specificity by a bacterial hitchhiker selection system.

    abstract::The design and selection of peptides targeting cellular proteins is challenging and often yields candidates with undesired properties. Therefore we deployed a new selection system based on the twin-arginine translocase (TAT) pathway of Escherichia coli, named hitchhiker translocation (HiT) selection. A pool of α-helix...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2014.03.002

    authors: Kükenshöner T,Wohlwend D,Niemöller C,Dondapati P,Speck J,Adeniran AV,Nieth A,Gerhardt S,Einsle O,Müller KM,Arndt KM

    更新日期:2014-06-01 00:00:00

  • Image analysis of helical objects: the Brandeis Helical Package.

    abstract::Although the fundamental steps in Fourier-based image analysis of electron micrographs of helical structures have not changed significantly since the techniques were developed 30 years ago, there have been developments which aid both the analysis itself and the interpretation of results. Increases in computational res...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1006/jsbi.1996.0027

    authors: Owen CH,Morgan DG,DeRosier DJ

    更新日期:1996-01-01 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

  • Analysis of immunolabeled cells by atomic force microscopy, optical microscopy, and flow cytometry.

    abstract::In this study we investigated the applicability of the (silver-enhanced) immunogold labeling method for atomic force microscopy. Human lymphocytes were labeled with anti-CD3 conjugated to fluorescein isothiocyanate and a secondary antibody (goat anti-mouse) linked with 1- or 30-nm colloidal gold particles. Silver enha...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1006/jsbi.1994.1004

    authors: Neagu C,van der Werf KO,Putman CA,Kraan YM,de Grooth BG,van Hulst NF,Greve J

    更新日期:1994-01-01 00:00:00

  • Broad yet high substrate specificity: the challenge of AAA+ proteins.

    abstract::AAA+ proteins remodel target substrates in an ATP-dependent manner, an activity that is of central importance for a plethora of cellular processes. While sharing a similar hexameric structure AAA+ proteins must exhibit differences in substrate recognition to fulfil their diverse biological functions. Here we describe ...

    journal_title:Journal of structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jsb.2003.10.009

    authors: Mogk A,Dougan D,Weibezahn J,Schlieker C,Turgay K,Bukau B

    更新日期:2004-04-01 00:00:00

  • Formation of biomineral iron oxides compounds in a Fe hyperaccumulator plant: Imperata cylindrica (L.) P. Beauv.

    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

    authors: Fuente V,Rufo L,Juárez BH,Menéndez N,García-Hernández M,Salas-Colera E,Espinosa A

    更新日期:2016-01-01 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

  • Crystal structure of inositol 1,3,4,5,6-pentakisphosphate 2-kinase from Cryptococcus neoformans.

    abstract::The fungal pathogen Cryptococcus neoformans is a causative agent of meningoencephalitis in humans. For its pathogenicity, the inositol polyphosphate biosynthetic pathway plays critical roles. Recently, Ipk1 from C. neoformans (CnIpk1) was identified as an inositol 1,3,4,5,6-pentakisphosphate 2-kinase that catalyzes th...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2017.09.004

    authors: Oh J,Lee DG,Bahn YS,Rhee S

    更新日期:2017-11-01 00:00:00

  • The LINKS motif zippers trans-acyltransferase polyketide synthase assembly lines into a biosynthetic megacomplex.

    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

    authors: Gay DC,Wagner DT,Meinke JL,Zogzas CE,Gay GR,Keatinge-Clay AT

    更新日期:2016-03-01 00:00:00

  • 7A projection map of the S-layer protein sbpA obtained with trehalose-embedded monolayer crystals.

    abstract::Two-dimensional crystallization on lipid monolayers is a versatile tool to obtain structural information of proteins by electron microscopy. An inherent problem with this approach is to prepare samples in a way that preserves the crystalline order of the protein array and produces specimens that are sufficiently flat ...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2007.06.002

    authors: Norville JE,Kelly DF,Knight TF Jr,Belcher AM,Walz T

    更新日期:2007-12-01 00:00:00

  • Two and three dimensional characterization of Zucchini Yellow Mosaic Virus induced structural alterations in Cucurbita pepo L. plants.

    abstract::Infection of plants by Zucchini Yellow Mosaic Virus (ZYMV) induces severe ultrastructural changes. The aim of this study was to investigate ultrastructural changes during ZYMV-infection in Cucurbita pepo L. plants on the two and three dimensional (2D and 3D) level and to correlate these changes with the spread of ZYMV...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2014.03.006

    authors: Zellnig G,Pöckl MH,Möstl S,Zechmann B

    更新日期:2014-05-01 00:00:00

  • Ultrastructure of familial amyloid polyneuropathy amyloid fibrils: examination with high-resolution electron microscopy.

    abstract::The ultrastructure of familial amyloid polyneuropathy (FAP) amyloid fibrils was examined with high-resolution electron microscopy and immunolabeling. Sural nerve biopsies from FAP (Met 30) patients as well as control tissues were prepared for thin-section observations. Extracellular spaces in the vicinity of myelinate...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1006/jsbi.1998.4052

    authors: Inoue S,Kuroiwa M,Saraiva MJ,Guimarães A,Kisilevsky R

    更新日期:1998-12-01 00:00:00

  • Mineralization and collagen orientation throughout aging at the vertebral endplate in the human lumbar spine.

    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

    authors: Paietta RC,Burger EL,Ferguson VL

    更新日期:2013-11-01 00:00:00

  • Conical tomography of freeze-fracture replicas: a method for the study of integral membrane proteins inserted in phospholipid bilayers.

    abstract::We have used conical tomography to study the structure of integral proteins in their phospholipid bilayer environments. Complete conical series were collected from replicas of the water channel aquaporin-0 (AQP0), a 6.6 nm side tetramer with a molecular weight of approximately 120 kDa that was purified and reconstitut...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2004.09.004

    authors: Lanzavecchia S,Cantele F,Bellon PL,Zampighi L,Kreman M,Wright E,Zampighi GA

    更新日期:2005-01-01 00:00:00

  • Capsids of tricorn protease studied by electron cryomicroscopy.

    abstract::Tricorn protease from the archaeon Thermoplasma acidophilum acts "downstream" of the proteasome; in conjunction with its aminopeptidase cofactors it converts peptides generated by the proteasome into free amino acids. The basic functional unit of Tricorn is a homohexamer of the 121-kDa subunit, 20 of which can assembl...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1006/jsbi.1999.4169

    authors: Walz J,Koster AJ,Tamura T,Baumeister W

    更新日期:1999-12-01 00:00:00

  • The canine baculum: the structure and mechanical properties of an unusual bone.

    abstract::The baculum is an extraskeletal bone located in the penis of a few species in several orders of mammals such as carnivores, insectivores, rodents, bats and primates. This study aims to describe the structure, architecture and mechanical properties of the canine baculum. To this end canine bacula from castrated and unc...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2011.06.006

    authors: Sharir A,Israeli D,Milgram J,Currey JD,Monsonego-Ornan E,Shahar R

    更新日期:2011-09-01 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

  • The use of electron tomography for structural analysis of disordered protein arrays.

    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

    authors: Taylor KA,Tang J,Cheng Y,Winkler H

    更新日期:1997-12-01 00:00:00

  • Change in single cystathionine β-synthase domain-containing protein from a bent to flat conformation upon adenosine monophosphate binding.

    abstract::Cystathionine β-synthase (CBS) domains are small intracellular modules that can act as binding domains for adenosine derivatives, and they may regulate the activity of associated enzymes or other functional domains. Among these, the single CBS domain-containing proteins, CBSXs, from Arabidopsis thaliana, have recently...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2013.04.013

    authors: Jeong BC,Park SH,Yoo KS,Shin JS,Song HK

    更新日期:2013-07-01 00:00:00

  • Cryo-EM analysis of the SctV cytosolic domain from the enteropathogenic E. coli T3SS injectisome.

    abstract::The bacterial injectisome and flagella both rely on type III secretion systems for their assembly. The syringe-like injectisome creates a continuous channel between the bacterium and the host cell, through which signal-modulating effector proteins are secreted. The inner membrane pore protein SctV controls the hierarc...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2020.107660

    authors: Majewski DD,Lyons BJE,Atkinson CE,Strynadka NCJ

    更新日期:2020-12-01 00:00:00

  • The bridge-region of the Ku superfamily is an atypical zinc ribbon domain.

    abstract::Members of the Ku superfamily are DNA-end-binding proteins involved in non-homologous end-joining (NHEJ) DNA repair. The published crystal structure of human Ku-DNA complex reveals a heterodimer that forms a ring around dsDNA by means of the Ku core modules. These modules contain a highly conserved seven-stranded β-ba...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2010.05.011

    authors: Krishna SS,Aravind L

    更新日期:2010-12-01 00:00:00

  • The two-step mode of growth in the scleractinian coral skeletons from the micrometre to the overall scale.

    abstract::It has been known since the 19th century that coral skeletons are built of aragonite crystals with taxonomy-linked arrangements, but the way by which each coral species controls this crystallization process remains an unsolved question. The problem became still more intriguing when it was shown that isotopic compositi...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2005.03.004

    authors: Cuif JP,Dauphin Y

    更新日期:2005-06-01 00:00:00

  • The rhodopsin-transducin complex houses two distinct rhodopsin molecules.

    abstract::Upon illumination the visual receptor rhodopsin (Rho) transitions to the activated form Rho(∗), which binds the heterotrimeric G protein, transducin (Gt) causing GDP to GTP exchange and Gt dissociation. Using succinylated concanavalin A (sConA) as a probe, we visualized native Rho dimers solubilized in 1mM n-dodecyl-β...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2013.02.014

    authors: Jastrzebska B,Ringler P,Palczewski K,Engel A

    更新日期:2013-05-01 00:00:00

  • Three different approaches for calculating the three-dimensional structure of microtubules decorated with kinesin motor domains.

    abstract::We have used three different electron microscopy approaches to calculate three-dimensional maps of tubulin assemblies decorated with the motor domain of kinesin. The approaches used were: (1) Tilt series reconstruction of negatively stained tubulin sheets. (2) Back-projection reconstruction of microtubules in ice. (3)...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1006/jsbi.1997.3851

    authors: Sosa H,Hoenger A,Milligan RA

    更新日期:1997-03-01 00:00:00

  • Structural and elemental characterization of heart cells grown in a collagen matrix.

    abstract::A novel preparation of spontaneously contracting heart cells embedded in a collagen strand provides an ideal experimental system for correlative structure-function experiments that utilize the techniques of electron microscopy, quantitative electron probe x-ray microanalysis (EPXMA) and imaging. Heart cells grown with...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/1047-8477(91)90061-z

    authors: LeFurgey A,Hawkey LA,Ingram P,Lieberman M

    更新日期:1991-02-01 00:00:00

  • Identification of the tailspike protein from the Salmonella newington phage epsilon 34 and partial characterization of its phage-associated properties.

    abstract::The lipopolysaccharide (LPS) of the Salmonella cell surface serves as the receptor for a very large number of bacterial viruses. The tailspike protein from these viruses recognizes the LPS as its initial receptor. It is proposed that the study of the P22 and epsilon 34 tailspike proteins could serve as a model for the...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1006/jsbi.1995.1053

    authors: Greenberg M,Dunlap J,Villafane R

    更新日期:1995-11-01 00:00:00

  • Crystallographic studies of ligand binding by Zn-alpha2-glycoprotein.

    abstract::Zn-alpha2-glycoprotein (ZAG) is a 41 kDa soluble protein that is present in most bodily fluids. The previously reported 2.8 A crystal structure of ZAG isolated from human serum demonstrated the structural similarity between ZAG and class I major histocompatibility complex (MHC) molecules and revealed a non-peptidic li...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2004.04.009

    authors: Delker SL,West AP Jr,McDermott L,Kennedy MW,Bjorkman PJ

    更新日期:2004-11-01 00:00:00

  • Structure of a hexameric RNA packaging motor in a viral polymerase complex.

    abstract::Packaging of the Cystovirus varphi8 genome into the polymerase complex is catalysed by the hexameric P4 packaging motor. The motor is located at the fivefold vertices of the icosahedrally symmetric polymerase complex, and the symmetry mismatch between them may be critical for function. We have developed a novel image-...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2006.08.021

    authors: Huiskonen JT,Jäälinoja HT,Briggs JA,Fuller SD,Butcher SJ

    更新日期:2007-05-01 00:00:00