Negatively stained 50 S ribosomal subunits of Escherichia coli.

Abstract:

:Ribosomes are large nucleoproteins of approximately 3 X 10(6) Mr. In contrast to helical or spherical nucleoproteins (viruses) of similar size (which consist of several hundred small asymmetric units reproduced by symmetry), ribosomes are completely asymmetric; therefore, the amount of structural information (defined by the number of independent image elements) necessarily increases from about 10 to 20 to about 1000 to 2000 (at resolutions of the order of 2 nm). With present techniques, only stained single particles can be studied in the electron microscope. Our published work on the 30 S subunit and on the 50 S subunit has demonstrated that three-dimensional reconstructions of stained single particles show a great number of structural details that are reproducible if the particles have the same orientation. One of the main results of this paper is the final proof of this reproducibility from detailed comparisons of individual 50 S subunits and of independent averages over a few (3 to 5) particles in the kidney or crown orientation; in the latter case, even after a chemical modification. The 50 S subunit is non-uniformly stained along the optical axis. It displays a complicated, stain-filled channel-like structure, within which is approximately the partial volume expected for the RNA. The particle shows an irregular but reproducible boundary surface against the stain. At several sites, the channel structure protrudes to the surface. Since the secondary structure of the RNA is well known, one might try to locate it in the subunit after chemical identification of its surface contacts (the 3' end of 23 S RNA and the 3' end of the 5 S RNA have been localized). Most interesting is a groove on the surface, which might accommodate the mRNA.

journal_name

J Mol Biol

authors

Hoppe W,Oettl H,Tietz HR

doi

10.1016/0022-2836(86)90366-9

subject

Has Abstract

pub_date

1986-11-20 00:00:00

pages

291-322

issue

2

eissn

0022-2836

issn

1089-8638

pii

0022-2836(86)90366-9

journal_volume

192

pub_type

杂志文章
  • Crystallographic study of one turn of G/C-rich B-DNA.

    abstract::The DNA decamer d(CCAGGCCTGG) has been studied by X-ray crystallography. At a nominal resolution of 1.6 A, the structure was refined to R = 16.9% using stereochemical restraints. The oligodeoxyribonucleotide forms a straight B-DNA double helix with crystallographic dyad symmetry and ten base-pairs per turn. In the cry...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90337-9

    authors: Heinemann U,Alings C

    更新日期:1989-11-20 00:00:00

  • Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities.

    abstract::The majority of archaeal viral genes are of unknown function hindering our understanding of the virus life cycle and viral interactions with their host. Here, we first describe functional characterization of ORF131b (gp17) and ORF436 (gp18) of Sulfolobus islandicus rod-shaped virus 2 (SIRV2), both encoding proteins of...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.03.013

    authors: Guo Y,Kragelund BB,White MF,Peng X

    更新日期:2015-06-19 00:00:00

  • Unwinding initiation by the viral RNA helicase NPH-II.

    abstract::Viral RNA helicases of the NS3/NPH-II group unwind RNA duplexes by processive, directional translocation on one of the duplex strands. The translocation is preceded by a poorly understood unwinding initiation phase. For NPH-II from vaccinia virus, unwinding initiation is rate limiting for the overall unwinding reactio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.11.045

    authors: Fairman-Williams ME,Jankowsky E

    更新日期:2012-02-03 00:00:00

  • X-ray structure of a water-soluble analog of the membrane protein phospholamban: sequence determinants defining the topology of tetrameric and pentameric coiled coils.

    abstract::Phospholamban (PLB) is a pentameric transmembrane protein that regulates the Ca(2+)-dependent ATPase SERCA2a in sarcoplasmic reticulum membranes. We previously described the computational design of a water-soluble variant of phospholamban, WSPLB, which reproduced many of the structural and functional properties of the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.02.040

    authors: Slovic AM,Stayrook SE,North B,Degrado WF

    更新日期:2005-05-06 00:00:00

  • Exploration of alternate catalytic mechanisms and optimization strategies for retroaldolase design.

    abstract::Designed retroaldolases have utilized a nucleophilic lysine to promote carbon-carbon bond cleavage of β-hydroxy-ketones via a covalent Schiff base intermediate. Previous computational designs have incorporated a water molecule to facilitate formation and breakdown of the carbinolamine intermediate to give the Schiff b...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.10.012

    authors: Bjelic S,Kipnis Y,Wang L,Pianowski Z,Vorobiev S,Su M,Seetharaman J,Xiao R,Kornhaber G,Hunt JF,Tong L,Hilvert D,Baker D

    更新日期:2014-01-09 00:00:00

  • Selection of Streptomyces griseus protease B mutants with desired alterations in primary specificity using a library screening strategy.

    abstract::Streptomyces griseus protease B (SGPB) has primary specificity for large hydrophobic residues. The protease is secreted in a promature form, and autocatalytic removal of the propeptide is essential for activity. We genetically substituted the P1 Leu at the promature junction of SGPB with Phe, Met, or Val and monitored...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0159

    authors: Sidhu SS,Borgford TJ

    更新日期:1996-03-29 00:00:00

  • Substitution of Asp114 or Arg116 in the fingers domain of moloney murine leukemia virus reverse transcriptase affects interactions with the template-primer resulting in decreased processivity.

    abstract::Reverse transcriptase, an essential retroviral DNA polymerase, replicates the single-stranded RNA genome of the retrovirus, producing a double-stranded DNA copy, which is subsequently integrated into the host's genome. Substitution of Ala for either Asp114 or Arg116, two highly conserved residues in the fingers domain...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4281

    authors: Gu J,Villanueva RA,Snyder CS,Roth MJ,Georgiadis MM

    更新日期:2001-01-12 00:00:00

  • Crystal structure of Thermotoga maritima 4-alpha-glucanotransferase and its acarbose complex: implications for substrate specificity and catalysis.

    abstract::4-alpha-Glucanotransferase (GTase) is an essential enzyme in alpha-1,4-glucan metabolism in bacteria and plants. It catalyses the transfer of maltooligosaccharides from an 1,4-alpha-D-glucan molecule to the 4-hydroxyl group of an acceptor sugar molecule. The crystal structures of Thermotoga maritima GTase and its comp...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00570-3

    authors: Roujeinikova A,Raasch C,Sedelnikova S,Liebl W,Rice DW

    更新日期:2002-08-02 00:00:00

  • The structure of Arabidopsis thaliana OST1 provides insights into the kinase regulation mechanism in response to osmotic stress.

    abstract::SnRK [SNF1 (sucrose non-fermenting-1)-related protein kinase] 2.6 [open stomata 1 (OST1)] is well characterized at molecular and physiological levels to control stomata closure in response to water-deficit stress. OST1 is a member of a family of 10 protein kinases from Arabidopsis thaliana (SnRK2) that integrates absc...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.09.041

    authors: Yunta C,Martínez-Ripoll M,Zhu JK,Albert A

    更新日期:2011-11-18 00:00:00

  • DNA topology-mediated regulation of transcription initiation from the tandem promoters of the ilvGMEDA operon of Escherichia coli.

    abstract::It is becoming increasingly clear that the intrinsic and protein-induced topological properties of the DNA helix influence transcriptional efficiency. In this report we describe the properties of two upstream activating regions that influence transcription from the non-overlapping tandem promoters of the ilvGMEDA oper...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90460-2

    authors: Pagel JM,Winkelman JW,Adams CW,Hatfield GW

    更新日期:1992-04-20 00:00:00

  • The major human structural IgE epitope of the Brazil nut allergen Ber e 1: a chimaeric and protein microarray approach.

    abstract::A protein microarray system containing different dilutions of 77 related and non-related proteins was used to show that IgE from subjects allergic to Brazil nut specifically recognise the seed 2S albumin protein (Ber e 1). Further, correctly folded chimaeric 2S albumin proteins containing structural epitope replacemen...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.08.065

    authors: Alcocer MJ,Murtagh GJ,Wilson PB,Progias P,Lin J,Archer DB

    更新日期:2004-10-22 00:00:00

  • Functional interactions among the His40, Glu58 and His92 catalysts of ribonuclease T1 as studied by double and triple mutants.

    abstract::We report on the functional interplay between the His40, Glu58 and His92 catalysts of ribonuclease T1. The kinetic properties of the single His40Ala, Glu58Ala and His92Gln mutants have been compared with those of the corresponding double and triple mutants. When His40, Glu58 and His92 are mutated separately or togethe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1078

    authors: Steyaert J,Wyns L

    更新日期:1993-02-05 00:00:00

  • Mitochondrial respiratory chain supercomplexes are destabilized in Barth Syndrome patients.

    abstract::Mutations in the human TAZ gene are associated with Barth Syndrome, an often fatal X-linked disorder that presents with cardiomyopathy and neutropenia. The TAZ gene encodes Tafazzin, a putative phospholipid acyltranferase that is involved in the remodeling of cardiolipin, a phospholipid unique to the inner mitochondri...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.06.057

    authors: McKenzie M,Lazarou M,Thorburn DR,Ryan MT

    更新日期:2006-08-18 00:00:00

  • Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage phi 29.

    abstract::The ATPase activity of the DNA packaging protein gp16 (gene product 16) of bacteriophage phi 29 was studied in the completely defined in-vitro assembly system. ATP was hydrolyzed to ADP and Pi in the packaging reaction that included purified proheads, DNA-gp3 and gp16. Approximately one molecule of ATP was used in the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90121-5

    authors: Guo P,Peterson C,Anderson D

    更新日期:1987-09-20 00:00:00

  • A novel mutation in the neurofibromatosis type 1 (NF1) gene promotes skipping of two exons by preventing exon definition.

    abstract::Using a protein truncation assay, we have identified a new mutation in the neurofibromatosis type 1 (NF1) gene that causes a severe defect in NF1 pre-mRNA splicing. The mutation, which consists of a G to A transition at position +1 of the 5' splice site of exon 12a, is associated with the loss of both exons 11 and 12a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4561

    authors: Fang LJ,Simard MJ,Vidaud D,Assouline B,Lemieux B,Vidaud M,Chabot B,Thirion JP

    更新日期:2001-04-13 00:00:00

  • Structure and mechanism of the magnesium-independent aromatic prenyltransferase CloQ from the clorobiocin biosynthetic pathway.

    abstract::CloQ is an aromatic prenyltransferase from the clorobiocin biosynthetic pathway of Streptomyces roseochromogenes var. oscitans. It is involved in the synthesis of the prenylated hydroxybenzoate moiety of the antibiotic, specifically catalyzing the attachment of a dimethylallyl moiety to 4-hydroxyphenylpyruvate. Herein...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.09.067

    authors: Metzger U,Keller S,Stevenson CE,Heide L,Lawson DM

    更新日期:2010-12-10 00:00:00

  • Cryo-electron tomography of clathrin-coated vesicles: structural implications for coat assembly.

    abstract::Clathrin-coated vesicles mediate vesicular traffic in cells. Three-dimensional image reconstructions of homogenous populations of in vitro assembled clathrin coats have yielded a molecular model for clathrin and its interactions with some of its partners. The intrinsic averaging required for those calculations has pre...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.10.036

    authors: Cheng Y,Boll W,Kirchhausen T,Harrison SC,Walz T

    更新日期:2007-01-19 00:00:00

  • Functional sites of the Ada regulatory protein of Escherichia coli. Analysis by amino acid substitutions.

    abstract::Specific cysteine residues at possible methyl acceptor sites of the Ada protein of Escherichia coli were converted to other amino acids by site-directed mutagenesis of the cloned ada gene of E. coli. Ada protein with the cysteine residue at 321 replaced by alanine was capable of accepting the methyl group from the met...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90137-4

    authors: Takano K,Nakabeppu Y,Sekiguchi M

    更新日期:1988-05-20 00:00:00

  • Crystal structure of Hsc20, a J-type Co-chaperone from Escherichia coli.

    abstract::Hsc20 is a 20 kDa J-protein that regulates the ATPase activity and peptide-binding specificity of Hsc66, an hsp70-class molecular chaperone. We report herein the crystal structure of Hsc20 from Escherichia coli determined to a resolution of 1.8 A using a combination of single isomorphous replacement (SIR) and multi-wa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4252

    authors: Cupp-Vickery JR,Vickery LE

    更新日期:2000-12-15 00:00:00

  • Experimental and theoretical studies of the effects of deoxyribose substitutions on the stability of the UUCG tetraloop.

    abstract::Experimental and theoretical thermodynamic studies of the consequences of 2'-hydroxyl substitution in the RNA UUCG tetraloop show distinct position dependence consistent with the diverse structural contexts of the four-loop ribose hydroxyls in this motif. The results suggest that even for simple substitutions, such as...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3547

    authors: Williams DJ,Hall KB

    更新日期:2000-03-17 00:00:00

  • Structural basis for ubiquitin recognition by SH3 domains.

    abstract::The SH3 domain is a protein-protein interaction module commonly found in intracellular signaling and adaptor proteins. The SH3 domains of multiple endocytic proteins have been recently implicated in binding ubiquitin, which serves as a signal for diverse cellular processes including gene regulation, endosomal sorting,...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.07.074

    authors: He Y,Hicke L,Radhakrishnan I

    更新日期:2007-10-12 00:00:00

  • The type I restriction endonuclease R.EcoR124I: over-production and biochemical properties.

    abstract::In this paper we describe a two-plasmid system which allows over-production of the R.EcoR124I restriction endonuclease. The endonuclease has been purified to homogeneity in milligram amounts and has been shown to be fully active for both restriction and modification. Unexpectedly, the enzyme was found to require only ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0217

    authors: Janscak P,Abadjieva A,Firman K

    更新日期:1996-04-19 00:00:00

  • Crystallization and preliminary X-ray data of a phleomycin-binding protein from Streptoalloteichus hindustanus.

    abstract::Large single crystals of a glycopeptide resistance protein encoded by the SH-ble gene from Streptoalloteichus hindustanus have been grown using vapor diffusion techniques with ammonium sulfate as the precipitant. The diffraction pattern extends to 2.0 A resolution. The crystals belong to space group P4(1)2(1)2 or P4(3...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90476-2

    authors: Rondeau JM,Cagnon C,Moras D,Masson JM

    更新日期:1989-06-05 00:00:00

  • Structural plasticity of the nuclear pore complex.

    abstract::The nuclear pore complex (NPC) is strategically located at continuous junctions of the inner and outer nuclear membranes to catalyze macromolecular transport, without impending the diffusion of small molecules. In this paper, the structural plasticity of 4412 NPCs in isolated nuclear envelopes has been evaluated, util...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(95)80050-6

    authors: Akey CW

    更新日期:1995-04-28 00:00:00

  • In vitro DNA tethering of HIV-1 integrase by the transcriptional coactivator LEDGF/p75.

    abstract::Although LEDGF/p75 is believed to act as a cellular cofactor of lentiviral integration by tethering integrase (IN) to chromatin, there is no good in vitro model to analyze this functionality. We designed an AlphaScreen assay to study how LEDGF/p75 modulates the interaction of human immunodeficiency virus type 1 IN wit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.03.073

    authors: McNeely M,Hendrix J,Busschots K,Boons E,Deleersnijder A,Gerard M,Christ F,Debyser Z

    更新日期:2011-07-29 00:00:00

  • Preliminary X-ray studies on an unspecific NAD(P)H dehydrogenase from human erythrocytes.

    abstract::Crystals of a relatively unspecific NAD(P)H dehydrogenase from human erythrocytes suitable for X-ray analysis have been grown. They belong to space group P4(1)2(1)2 or its enantiomorph P4(3)2(1)2 with unit cell dimensions: a = b = 79.3 A and c = 38.1 A. The asymmetric unit contains one molecule of Mr 18,000. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90093-7

    authors: Pai EF

    更新日期:1984-04-25 00:00:00

  • The 2.0A resolution structure of the catalytic portion of a cyanobacterial membrane-bound manganese superoxide dismutase.

    abstract::Cyanobacteria are shown to be unique in containing membrane-bound manganese superoxide dismutases (MnSOD). They are homodimeric type 2 membrane proteins that protect this phototrophic organism against oxidative stress. We have determined, for the first time, the 2.0A resolution structure of the catalytic portion of th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00624-1

    authors: Atzenhofer W,Regelsberger G,Jacob U,Peschek G,Furtmüller P,Huber R,Obinger C

    更新日期:2002-08-16 00:00:00

  • Influenza Hemifusion Phenotype Depends on Membrane Context: Differences in Cell-Cell and Virus-Cell Fusion.

    abstract::Influenza viral entry into the host cell cytoplasm is accomplished by a process of membrane fusion mediated by the viral hemagglutinin protein. Hemagglutinin acts in a pH-triggered fashion, inserting a short fusion peptide into the host membrane followed by refolding of a coiled-coil structure to draw the viral envelo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2018.01.006

    authors: Zawada KE,Okamoto K,Kasson PM

    更新日期:2018-03-02 00:00:00

  • Mutations in the conserved P loop perturb the conformation of two structural elements in the peptidyl transferase center of 23 S ribosomal RNA.

    abstract::Evidence is presented for the participation of the P loop (nucleotides G2250-C2254) of 23 S rRNA in establishing the tertiary structure of the peptidyl transferase center. Single base substitutions were introduced into the P loop, which participates in peptide bond formation through direct interaction with the CCA end...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2410

    authors: Gregory ST,Dahlberg AE

    更新日期:1999-01-29 00:00:00

  • Crystallization of and preliminary X-ray data for the mouse major urinary protein and rat alpha-2u globulin.

    abstract::Crystals of the mouse major urinary protein (MUP) and rat alpha-2u globulin (AMG) have been grown from solutions of polyethylene glycol 3350 and CdCl2, respectively. The crystals differ both in their morphologies and space groups but have very similar unit cell sizes. AMG crystallized in P2(1) (a = 56.6 A, b = 103.8 A...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90258-8

    authors: Böcskei Z,Findlay JB,North AC,Phillips SE,Somers WS,Wright CE,Lionetti C,Tirindelli R,Cavaggioni A

    更新日期:1991-04-20 00:00:00