Structure of the Ni/Fe-S protein subcomponent of the acetyl-CoA decarbonylase/synthase complex from Methanosarcina thermophila at 26-A resolution.

Abstract:

:The acetyl-CoA decarbonylase/synthase (ACDS) complex is responsible for synthesis and cleavage of acetyl-CoA in methanogens. The complex is composed of five different subunits, with a probable stoichiometry of alpha(8)beta(8)gamma(8)delta(8)epsilon(8). The native molecular mass of a subcomponent of the ACDS complex from Methanosarcina thermophila, the Ni/Fe-S protein containing the 90-kDa alpha and 19-kDa epsilon subunits, was determined by scanning transmission electron microscopy. A value of 218.6 +/- 19.6 kDa (n = 566) was obtained, thus establishing that the oligomeric structure of this subcomponent is alpha(2)epsilon(2). The three-dimensional structure of alpha(2)epsilon(2) was determined at 26-A resolution by analysis of a large number of electron microscopic images of negatively stained, randomly oriented particles. The alpha(2)epsilon(2) subcomponent has a globular appearance, 110 A in diameter, and consists of two large, hemisphere-like masses that surround a hollow internal cavity. The two large masses are connected along one face by a bridge-like structure and have relatively less protein density joining them at other positions. The internal cavity has four main openings to the outside, one of which is directly adjacent to the bridge. The results are consistent with a structure in which the large hemispheric masses are assigned to the two alpha subunits, with epsilon(2) as the bridge forming a structural link between them. The structure of the alpha(2)epsilon(2) subcomponent is discussed in connection with biochemical data from gel filtration, crosslinking, and dissociation experiments and in the context of its function as a major component of the ACDS complex.

journal_name

J Struct Biol

authors

Kocsis E,Kessel M,DeMoll E,Grahame DA

doi

10.1006/jsbi.1999.4163

keywords:

subject

Has Abstract

pub_date

1999-12-15 00:00:00

pages

165-74

issue

2

eissn

1047-8477

issn

1095-8657

pii

S1047-8477(99)94163-1

journal_volume

128

pub_type

杂志文章
  • Gold-tagged RNA-A probe for macromolecular assemblies.

    abstract::Ribonucleic acids (RNAs) play a key role in many fundamental life processes. These polymers are often found complexed with proteins in extremely large particles whose molecular mass may reach several millions of daltons (e.g., ribosomes, spliceosomes, and viruses). Structural studies of such RNA-protein complexes shou...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1006/jsbi.1999.4134

    authors: Medalia O,Heim M,Guckenberger R,Sperling R,Sperling J

    更新日期:1999-09-01 00:00:00

  • 3D morphology of the human hepatic ferritin mineral core: new evidence for a subunit structure revealed by single particle analysis of HAADF-STEM images.

    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

    authors: Pan YH,Sader K,Powell JJ,Bleloch A,Gass M,Trinick J,Warley A,Li A,Brydson R,Brown A

    更新日期:2009-04-01 00:00:00

  • Blotting-free and lossless cryo-electron microscopy grid preparation from nanoliter-sized protein samples and single-cell extracts.

    abstract::We present a sample preparation method for cryo-electron microscopy (cryo-EM) that requires only 3-20nL of sample to prepare a cryo-EM grid, depending on the protocol used. The sample is applied and spread on the grid by a microcapillary. The procedure does not involve any blotting steps, and real-time monitoring allo...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2016.11.002

    authors: Arnold SA,Albiez S,Bieri A,Syntychaki A,Adaixo R,McLeod RA,Goldie KN,Stahlberg H,Braun T

    更新日期:2017-03-01 00:00:00

  • Charge contrast imaging of biomaterials in a variable pressure scanning electron microscope.

    abstract::Charge contrast imaging (CCI) is a dynamic phenomenon recently reported in insulating and semiconducting materials imaged with low vacuum or variable pressure scanning electron microscopes (SEM). Data presented in this paper illustrates that CCI can also be applied to biominerals and biological soft-tissues and that u...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2006.04.004

    authors: Clode PL

    更新日期:2006-09-01 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

  • 3D imaging of diatoms with ion-abrasion scanning electron microscopy.

    abstract::Ion-abrasion scanning electron microscopy (IASEM) takes advantage of focused ion beams to abrade thin sections from the surface of bulk specimens, coupled with SEM to image the surface of each section, enabling 3D reconstructions of subcellular architecture at approximately 30nm resolution. Here, we report the first a...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2009.02.014

    authors: Hildebrand M,Kim S,Shi D,Scott K,Subramaniam S

    更新日期:2009-06-01 00:00:00

  • Expedited approaches to whole cell electron tomography and organelle mark-up in situ in high-pressure frozen pancreatic islets.

    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

    authors: Noske AB,Costin AJ,Morgan GP,Marsh BJ

    更新日期:2008-03-01 00:00:00

  • Detecting molecular interactions that stabilize, activate and guide ligand-binding of the sodium/proton antiporter MjNhaP1 from Methanococcus jannaschii.

    abstract::Integral membrane proteins are involved in virtually every cellular process. Precisely regulating these machineries would allow controlling many human and vertebrate diseases. Embedded into cellular membranes, membrane proteins establish molecular interactions that sensitively react to environmental changes and to mol...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2007.02.010

    authors: Kedrov A,Wegmann S,Smits SH,Goswami P,Baumann H,Muller DJ

    更新日期:2007-08-01 00:00:00

  • Automated image acquisition and processing using a new generation of 4K x 4K CCD cameras for cryo electron microscopic studies of macromolecular assemblies.

    abstract::We have previously reported the development of AutoEM, a software package for semi-automated acquisition of data from a transmission electron microscope. In continuing efforts to improve the speed of structure determination of macromolecular assemblies by electron microscopy, we report here on the performance of a new...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/s1047-8477(03)00124-2

    authors: Zhang P,Borgnia MJ,Mooney P,Shi D,Pan M,O'Herron P,Mao A,Brogan D,Milne JL,Subramaniam S

    更新日期:2003-08-01 00:00:00

  • A method for establishing the handedness of biological macromolecules.

    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

    authors: Belnap DM,Olson NH,Baker TS

    更新日期:1997-10-01 00:00:00

  • Cryo X-ray microscope with flat sample geometry for correlative fluorescence and nanoscale tomographic imaging.

    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

    authors: Schneider G,Guttmann P,Rehbein S,Werner S,Follath R

    更新日期:2012-02-01 00:00:00

  • Application of isotope exchange based mass spectrometry to understand the mechanism of inhibition of sickle hemoglobin polymerization upon oxygenation.

    abstract::Sickle hemoglobin (HbS) polymerization initiates in the deoxy state with the binding of hydrophobic patch formed by the isopropyl group of βVal6 residue of a hemoglobin tetramer with the hydrophobic pocket of another tetramer, whose hydrophobic patch binds to the hydrophobic groove of a third molecule. Subsequent elon...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2017.04.009

    authors: Das R,Mitra A,Bhat V,Mandal AK

    更新日期:2017-07-01 00:00:00

  • Structural and dynamics studies of the TetR family protein, CprB from Streptomyces coelicolor in complex with its biological operator sequence.

    abstract::In Streptomycetes, tetracycline repressor family of transcription regulators (TetR-FTRs) controls various biological processes including antibiotic biosynthesis, cellular morphology and innate resistance. Here, we focus on understanding the structural basis of transcription regulation by CprB, a member of TetR-FTRs fr...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2017.03.006

    authors: Bhukya H,Jana AK,Sengupta N,Anand R

    更新日期:2017-05-01 00:00:00

  • Low resolution solution structure of an enzymatic active AhpC10:AhpF2 ensemble of the Escherichia coli Alkyl hydroperoxide Reductase.

    abstract::The ability of bacteria to combat oxidative stress is imperative for their survival. The Alkyl hydroperoxide Reductase (AhpR) system, composed of the AhpC and AhpF proteins, is one of the dominant antioxidant defense systems required for scavenging hydrogen peroxide and organic peroxide. Therefore, it is necessary to ...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2015.11.004

    authors: Kamariah N,Nartey W,Eisenhaber B,Eisenhaber F,Grüber G

    更新日期:2016-01-01 00:00:00

  • A new HIV-1 Rev structure optimizes interaction with target RNA (RRE) for nuclear export.

    abstract::HIV-1 Rev mediates the nuclear export of unspliced and partially-spliced viral transcripts for the production of progeny genomes and structural proteins. In this process, four (or more) copies of Rev assemble onto a highly-structured 351-nt region in such viral transcripts, the Rev response element (RRE). How this occ...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2018.03.011

    authors: Watts NR,Eren E,Zhuang X,Wang YX,Steven AC,Wingfield PT

    更新日期:2018-08-01 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

  • Looking into live cells with in-cell NMR spectroscopy.

    abstract::In-cell NMR spectroscopy has gained recent popularity since it provides means to analyze the conformational and functional properties of proteins inside living cells and at atomic resolution. High-resolution in-cell NMR spectroscopy was originally established in bacterial cells and based on a rationale that relies on ...

    journal_title:Journal of structural biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jsb.2007.04.001

    authors: Selenko P,Wagner G

    更新日期:2007-05-01 00:00:00

  • Crystallographic Characterization of the DNA-Binding Domain of Interferon Regulatory Factor-2 Complexed with DNA.

    abstract::Interferon regulatory factors (IRFs) are transcription factors for interferon-related genes, which manifest both antiviral and tumor-suppressor activities and regulate cell growth in response to DNA damage. For the transcription initiation of the interferon-beta gene, IRFs form a macromolecular assembly bound to the p...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1006/jsbi.1998.3970

    authors: Kusumoto M,Fujii Y,Tsukuda Y,Ohira T,Kyougoku Y,Taniguchi T,Hakoshima T

    更新日期:1998-01-01 00:00:00

  • Native structure of a retroviral envelope protein and its conformational change upon interaction with the target cell.

    abstract::Enveloped viruses enter their host cells by membrane fusion. The process of attachment and fusion in retroviruses is mediated by a single viral envelope glycoprotein (Env). Conformational changes of Env in the course of fusion are a focus of intense studies. Here we provide further insight into the changes occurring i...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2016.06.017

    authors: Riedel C,Vasishtan D,Siebert CA,Whittle C,Lehmann MJ,Mothes W,Grünewald K

    更新日期:2017-02-01 00:00:00

  • An approach to automated acquisition of cryoEM images from lacey carbon grids.

    abstract::An approach to automated acquisition of cryoEM image data from lacey carbon grids using the Leginon program is described. Automated liquid nitrogen top up of the specimen holder dewar was used as a step towards full automation, without operator intervention during the course of data collection. During cryoEM studies o...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2010.08.014

    authors: Nicholson WV,White H,Trinick J

    更新日期:2010-12-01 00:00:00

  • The structural characteristics of mononuclear-macrophage membrane observed by atomic force microscopy.

    abstract::Mononuclear macrophages are important immune cells in the organisms. The complicated membrane structure underlying the diverse functions of mononuclear-macrophage has been largely unresolved. As a representative of monocyte-derived macrophages, the membrane structure of PMA differentiated THP-1 cells was comprehensive...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2019.04.002

    authors: Tian Y,Wu Y,Liu L,He L,Gao J,Zhou L,Yu F,Yu S,Wang H

    更新日期:2019-06-01 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

  • Reversible swelling of SBMV is associated with reversible disordering.

    abstract::The structures of the compact and swollen southern bean mosaic virus (SBMV) particles have been compared by X-ray diffraction and proton magnetic resonance (PMR). Small-angle X-ray scattering showed that removal of divalent cations at alkaline pH causes the particle diameter to increase from 289Å in the native SBMV by...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2017.06.003

    authors: Li J,Fricks C,Rayment I,Caspar DLD

    更新日期:2017-12-01 00:00:00

  • Higher order assembling of the mycobacterial polar growth factor DivIVA/Wag31.

    abstract::DivIVA or Wag31, which is an essential pole organizing protein in mycobacteria, can self-assemble at the negatively curved side of the membrane at the growing pole to form a higher order structural scaffold for maintaining cellular morphology and localizing various target proteins for cell-wall biogenesis. The structu...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2019.107429

    authors: Choukate K,Gupta A,Basu B,Virk K,Ganguli M,Chaudhuri B

    更新日期:2020-02-01 00:00:00

  • Performance evaluation of image processing algorithms on the GPU.

    abstract::The graphics processing unit (GPU), which originally was used exclusively for visualization purposes, has evolved into an extremely powerful co-processor. In the meanwhile, through the development of elaborate interfaces, the GPU can be used to process data and deal with computationally intensive applications. The spe...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2008.07.006

    authors: Castaño-Díez D,Moser D,Schoenegger A,Pruggnaller S,Frangakis AS

    更新日期:2008-10-01 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

  • Single-step antibody-based affinity cryo-electron microscopy for imaging and structural analysis of macromolecular assemblies.

    abstract::Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies (i.e., protein complexes and viruses). Although single particle cryo-EM requires less concentrated and smaller amounts of samples than X-ray crystallography, it remains challenging to stu...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2014.04.006

    authors: Yu G,Vago F,Zhang D,Snyder JE,Yan R,Zhang C,Benjamin C,Jiang X,Kuhn RJ,Serwer P,Thompson DH,Jiang W

    更新日期:2014-07-01 00:00:00

  • Biochemical characterization of the skeletal matrix of the massive coral, Porites australiensis - The saccharide moieties and their localization.

    abstract::To construct calcium carbonate skeletons of sophisticated architecture, scleractinian corals secrete an extracellular skeletal organic matrix (SOM) from aboral ectodermal cells. The SOM, which is composed of proteins, saccharides, and lipids, performs functions critical for skeleton formation. Even though polysacchari...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1016/j.jsb.2018.05.011

    authors: Takeuchi T,Plasseraud L,Ziegler-Devin I,Brosse N,Shinzato C,Satoh N,Marin F

    更新日期:2018-09-01 00:00:00

  • Automatic alignment of transmission electron microscope tilt series without fiducial markers.

    abstract::Accurate image alignment is needed for computing three-dimensional reconstructions from transmission electron microscope tilt series. So far, the best results have been obtained by using colloidal gold beads as fiducial markers. If their use has not been possible for some reason, the only option has been the automatic...

    journal_title:Journal of structural biology

    pub_type: 杂志文章

    doi:10.1006/jsbi.2001.4443

    authors: Brandt S,Heikkonen J,Engelhardt P

    更新日期:2001-12-01 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