A conformational switch involved in maturation of Staphylococcus aureus bacteriophage 80α capsids.


:Bacteriophages are involved in many aspects of the spread and establishment of virulence factors in Staphylococcus aureus, including the mobilization of genetic elements known as S. aureus pathogenicity islands (SaPIs), which carry genes for superantigen toxins and other virulence factors. SaPIs are packaged into phage-like transducing particles using proteins supplied by the helper phage. We have used cryo-electron microscopy and icosahedral reconstruction to determine the structures of the procapsid and the mature capsid of 80α, a bacteriophage that can mobilize several different SaPIs. The 80α capsid has T=7 icosahedral symmetry with the capsid protein organized into pentameric and hexameric clusters that interact via prominent trimeric densities. The 80α capsid protein was modeled based on the capsid protein fold of bacteriophage HK97 and fitted into the 80α reconstructions. The models show that the trivalent interactions are mediated primarily by a 22-residue β hairpin structure called the P loop that is not found in HK97. Capsid expansion is associated with a conformational switch in the spine helix that is propagated throughout the subunit, unlike the domain rotation mechanism in phage HK97 or P22.


J Mol Biol


Spilman MS,Dearborn AD,Chang JR,Damle PK,Christie GE,Dokland T




Has Abstract


2011-01-21 00:00:00














  • Bacterial Signaling to the Nervous System through Toxins and Metabolites.

    abstract::Mammalian hosts interface intimately with commensal and pathogenic bacteria. It is increasingly clear that molecular interactions between the nervous system and microbes contribute to health and disease. Both commensal and pathogenic bacteria are capable of producing molecules that act on neurons and affect essential ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: Yang NJ,Chiu IM

    更新日期:2017-03-10 00:00:00

  • The SH3 domain of nebulin binds selectively to type II peptides: theoretical prediction and experimental validation.

    abstract::Nebulin, a giant modular protein from muscle, is thought to act as a molecular ruler in sarcomere assembly. The C terminus of nebulin, located in the sarcomere Z-disk, comprises an SH3 domain, a module well known for its role in protein/protein interactions. SH3 domains are known to recognize proline-rich ligands, whi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Politou AS,Spadaccini R,Joseph C,Brannetti B,Guerrini R,Helmer-Citterich M,Salvadori S,Temussi PA,Pastore A

    更新日期:2002-02-15 00:00:00

  • Splicing of a cap-proximal human Papillomavirus 16 E6E7 intron promotes E7 expression, but can be restrained by distance of the intron from its RNA 5' cap.

    abstract::Human papillomavirus 16 (HPV16) E6E7 pre-mRNA is bicistronic and has an intron in the E6 coding region with one 5' splice site and two alternative 3' splice sites, which produce E6(*)I and E6(*)II, respectively. If this intron remains unspliced, the resulting E6E7 mRNA expresses oncogenic E6. We found for the first ti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Zheng ZM,Tao M,Yamanegi K,Bodaghi S,Xiao W

    更新日期:2004-04-09 00:00:00

  • Characterization of in vitro and in vivo mutations in non-conserved nucleotides in the ribosomal RNA recognition domain for the ribotoxins ricin and sarcin and the translation elongation factors.

    abstract::The sarcin/ricin domain in 23 S/28 S rRNA is crucial for ribosome function, since it constitutes at least part of the binding site for the elongation factors and hence is essential for binding aminoacyl-tRNA and for translocation. The domain is also the site of action of ricin and sarcin and analysis of the effect of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Macbeth MR,Wool IG

    更新日期:1999-01-15 00:00:00

  • NMR structure of the HIV-1 regulatory protein VPR.

    abstract::The human immunodeficiency virus type 1 (HIV-1) genome encodes a highly conserved regulatory gene product, Vpr (96 residues, 14kDa), which is incorporated into virions. In the infected cells, Vpr, expressed late in the virus cycle, is believed to function in the early phases of HIV-1 replication, such as nuclear migra...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Morellet N,Bouaziz S,Petitjean P,Roques BP

    更新日期:2003-03-14 00:00:00

  • Minor structural changes in a mutated human melanoma antigen correspond to dramatically enhanced stimulation of a CD4+ tumor-infiltrating lymphocyte line.

    abstract::While most immunotherapies for cancer have focused on eliciting specific CD8+ cytotoxic T lymphocyte killing of tumor cells, a mounting body of evidence suggests that stimulation of anti-tumor CD4+ T cell help may be required for highly effective therapy. Several MHC class II-restricted tumor antigens that specificall...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Sundberg EJ,Sawicki MW,Southwood S,Andersen PS,Sette A,Mariuzza RA

    更新日期:2002-05-31 00:00:00

  • Prolonged Ca2+ and force transients in myosin RLC transgenic mouse fibers expressing malignant and benign FHC mutations.

    abstract::Clinical studies have revealed that mutations in the ventricular myosin regulatory light chain (RLC) lead to the development of familial hypertrophic cardiomyopathy (FHC), an autosomal dominant disease characterized by left ventricular hypertrophy, myofibrillar disarray and sudden cardiac death. While mutations in oth...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Wang Y,Xu Y,Kerrick WG,Wang Y,Guzman G,Diaz-Perez Z,Szczesna-Cordary D

    更新日期:2006-08-11 00:00:00

  • Defining the peptide nucleic acids (PNA) length requirement for PNA binding-induced transcription and gene expression.

    abstract::Induction of gene expression has great potential in the treatment of many human diseases. Peptide nucleic acid (PNA) as a novel DNA-binding reagent provides an ideal system to induce gene-specific expression. In our recent studies, we have demonstrated that PNA bound to double-stranded DNA targets and, therefore, gene...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Wang G,Jing K,Balczon R,Xu X

    更新日期:2001-11-09 00:00:00

  • Influence of amino acid and peptide counterions on the conformation of DNA.

    abstract::We describe fibre diffraction studies on the interaction of DNA with different amino acids and peptides. The B form of DNA, with ten base-pairs per turn, is always found at high levels of humidity. We suggest that this pitch is observed because the DNA molecules are maintained in a straight position. In solution, the ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Campos JL,Portugal J,Subirana JA,Mayer R

    更新日期:1986-02-05 00:00:00

  • Halogenated benzenes bound within a non-polar cavity in T4 lysozyme provide examples of I...S and I...Se halogen-bonding.

    abstract::We showed earlier that the mutation of Leu99 to alanine in bacteriophage T4 lysozyme creates an internal cavity of volume approximately 150 A(3) that binds benzene and a variety of other ligands. As such, this cavity provides an excellent target to study protein-ligand interaction. Here, we use low-temperature crystal...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Liu L,Baase WA,Matthews BW

    更新日期:2009-01-16 00:00:00

  • Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif.

    abstract::Many viruses employ ATP-powered motors for genome packaging. We combined genetic, biochemical, and single-molecule techniques to confirm the predicted Walker-B ATP-binding motif in the phage λ motor and to investigate the roles of the conserved residues. Most changes of the conserved hydrophobic residues resulted in >...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: delToro D,Ortiz D,Ordyan M,Pajak J,Sippy J,Catala A,Oh CS,Vu A,Arya G,Smith DE,Catalano CE,Feiss M

    更新日期:2019-11-08 00:00:00

  • The role of DNA structure and dynamics in the recognition of bovine papillomavirus E2 protein target sequences.

    abstract::The papillomavirus E2 transcription and replication factors bind to the DNA consensus ACCGN(4)CGGT sequence (E2-BS), through both direct and indirect readout mechanisms. The two symmetric half-sites ACCG.CGGT are highly conserved in the genomes and are hydrogen bound with E2. Although E2 does not contact the N4 spacer...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Djuranovic D,Oguey C,Hartmann B

    更新日期:2004-06-11 00:00:00

  • Quasi-symmetry in the cryo-EM structure of EmrE provides the key to modeling its transmembrane domain.

    abstract::Small multidrug resistance (SMR) transporters contribute to bacterial resistance by coupling the efflux of a wide range of toxic aromatic cations, some of which are commonly used as antibiotics and antiseptics, to proton influx. EmrE is a prototypical small multidrug resistance transporter comprising four transmembran...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Fleishman SJ,Harrington SE,Enosh A,Halperin D,Tate CG,Ben-Tal N

    更新日期:2006-11-17 00:00:00

  • Whither Ribosome Structure and Dynamics Research? (A Perspective).

    abstract::As high-resolution cryogenic electron microscopy (cryo-EM) structures of ribosomes proliferate, at resolutions that allow atomic interactions to be visualized, this article attempts to give a perspective on the way research on ribosome structure and dynamics may be headed, and particularly the new opportunities we hav...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: Frank J

    更新日期:2016-09-11 00:00:00

  • Unwinding single RNA molecules using helicases involved in eukaryotic translation initiation.

    abstract::The small (40 S) subunit of the eukaryotic ribosome may have to scan more than 2000 nucleotides (>600 nm) from its 5'cap recruiting point on an mRNA molecule before initiating on a translation start codon. As with many other processes in living cells, including transcription, editing, mRNA splicing, pre-rRNA processin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Marsden S,Nardelli M,Linder P,McCarthy JE

    更新日期:2006-08-11 00:00:00

  • Investigating the high affinity and low sequence specificity of calmodulin binding to its targets.

    abstract::Calmodulin (CaM) is a calcium binding protein that regulates a wide range of enzymes. Recently the structures of a number of complexes between CaM and synthetic target peptides have been determined. The peptides correspond to the CaM-binding domain of skeletal and smooth muscle myosin light-chain kinase (MLCK) and cal...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Afshar M,Caves LS,Guimard L,Hubbard RE,Calas B,Grassy G,Haiech J

    更新日期:1994-12-16 00:00:00

  • Dynamics may significantly influence the estimation of interatomic distances in biomolecular X-ray structures.

    abstract::Atomic positions obtained by X-ray crystallography are time and space averages over many molecules in the crystal. Importantly, interatomic distances, calculated between such average positions and frequently used in structural and mechanistic analyses, can be substantially different from the more appropriate time-aver...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kuzmanic A,Kruschel D,van Gunsteren WF,Pannu NS,Zagrovic B

    更新日期:2011-08-05 00:00:00

  • Conformational properties of the aggregation precursor state of HypF-N.

    abstract::The conversion of specific proteins or protein fragments into insoluble, ordered fibrillar aggregates is a fundamental process in protein chemistry, biology, medicine and biotechnology. As this structural conversion seems to be a property shared by many proteins, understanding the mechanism of this process will be of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Campioni S,Mossuto MF,Torrassa S,Calloni G,de Laureto PP,Relini A,Fontana A,Chiti F

    更新日期:2008-06-06 00:00:00

  • Protein titration in the crystal state.

    abstract::Proteins are complex structures whose overall stability critically depends on a delicate balance of numerous interactions of similar strength, which are markedly influenced by their environment. Here, we present an analysis of the effect of pH on a protein structure in the crystalline state using RNase A as a model sy...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Berisio R,Lamzin VS,Sica F,Wilson KS,Zagari A,Mazzarella L

    更新日期:1999-10-01 00:00:00

  • The serine protease inhibitor canonical loop conformation: examples found in extracellular hydrolases, toxins, cytokines and viral proteins.

    abstract::Methods for the prediction of protein function from structure are of growing importance in the age of structural genomics. Here, we focus on the problem of identifying sites of potential serine protease inhibitor interactions on the surface of proteins of known structure. Given that there is no sequence conservation w...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Jackson RM,Russell RB

    更新日期:2000-02-18 00:00:00

  • The 1.2 A structure of a novel quorum-sensing protein, Bacillus subtilis LuxS.

    abstract::In bacteria, the regulation of gene expression in response to changes in cell density is called quorum sensing. The autoinducer-2 production protein LuxS, is involved in a novel quorum-sensing system and is thought to catalyse the degradation of S-ribosylhomocysteine to homocysteine and the autoinducer molecule 4,5-di...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ruzheinikov SN,Das SK,Sedelnikova SE,Hartley A,Foster SJ,Horsburgh MJ,Cox AG,McCleod CW,Mekhalfia A,Blackburn GM,Rice DW,Baker PJ

    更新日期:2001-10-12 00:00:00

  • Unveiling hidden catalytic contributions of the conserved His/Trp-III in tyrosine recombinases: assembly of a novel active site in Flp recombinase harboring alanine at this position.

    abstract::The catalytic pentad of tyrosine recombinases, that assists the tyrosine nucleophile, includes a conserved histidine/tryptophan (His/Trp-III). Flp and Cre harbor tryptophan at this position; most of their kin recombinases display histidine. Contrary to the conservation rule, Flp(W330F) is a much stronger recombinase t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ma CH,Kwiatek A,Bolusani S,Voziyanov Y,Jayaram M

    更新日期:2007-04-20 00:00:00

  • Structural flexibility of the N-terminal beta-barrel domain of 15-lipoxygenase-1 probed by small angle X-ray scattering. Functional consequences for activity regulation and membrane binding.

    abstract::Mammalian lipoxygenases form a heterogeneous family of lipid peroxidizing enzymes, which have been implicated in synthesis of inflammatory mediators, in cell development and in the pathogenesis of various diseases (atherosclerosis, osteoporosis) with major health political importance. The crystal structures of two pla...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Hammel M,Walther M,Prassl R,Kuhn H

    更新日期:2004-10-29 00:00:00

  • Exploring the structural dynamics of the E.coli chaperonin GroEL using translation-libration-screw crystallographic refinement of intermediate states.

    abstract::Large rigid-body domain movements are critical to GroEL-mediated protein folding, especially apical domain elevation and twist associated with the formation of a folding chamber upon binding ATP and co-chaperonin GroES. Here, we have modeled the anisotropic displacements of GroEL domains from various crystallized stat...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Chaudhry C,Horwich AL,Brunger AT,Adams PD

    更新日期:2004-09-03 00:00:00

  • Refined structure of the nicotinic acetylcholine receptor at 4A resolution.

    abstract::We present a refined model of the membrane-associated Torpedo acetylcholine (ACh) receptor at 4A resolution. An improved experimental density map was obtained from 342 electron images of helical tubes, and the refined structure was derived to an R-factor of 36.7% (R(free) 37.9%) by standard crystallographic methods, a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Unwin N

    更新日期:2005-03-04 00:00:00

  • Two secretory protein genes in Chironomus tentans have arisen by gene duplication and exhibit different developmental expression patterns.

    abstract::The salivary gland cells in the dipteran Chironomus tentans produce approximately 15 different secretory proteins, with relative molecular masses ranging between 1 x 10(4) and 1 x 10(6). Together these proteins form two types of extra corporal tubes, a larval protective housing and feeding tube or a pupation tube. The...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Galli J,Wieslander L

    更新日期:1993-05-20 00:00:00

  • Calcium-dependent homoassociation of E-cadherin by NMR spectroscopy: changes in mobility, conformation and mapping of contact regions.

    abstract::Cadherins are calcium-dependent cell surface proteins that mediate homophilic cellular adhesion. The calcium-induced oligomerization of the N-terminal two domains of epithelial cadherin (ECAD12) was followed by NMR spectroscopy in solution over a large range of protein (10 microM-5 mM) and calcium (0-5 mM) concentrati...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Häussinger D,Ahrens T,Sass HJ,Pertz O,Engel J,Grzesiek S

    更新日期:2002-12-06 00:00:00

  • Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae.

    abstract::Riboswitches are complex folded RNA domains found in noncoding regions of mRNA that regulate gene expression upon small molecule binding. Recently, Breaker and coworkers reported a tandem aptamer riboswitch (VCI-II) that binds glycine cooperatively. Here, we use hydroxyl radical footprinting and small-angle X-ray scat...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lipfert J,Das R,Chu VB,Kudaravalli M,Boyd N,Herschlag D,Doniach S

    更新日期:2007-02-02 00:00:00

  • Specification of DNA replication origins and genomic base composition in fission yeasts.

    abstract::In the "Replicon Theory", Jacob, Brenner and Cuzin proposed the existence of replicators and initiators as the two major actors in DNA replication. Over the years, many protein components of initiators have been shown to be conserved in different organisms during evolution. By contrast, replicator DNA sequences (often...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: Mojardín L,Vázquez E,Antequera F

    更新日期:2013-11-29 00:00:00

  • The Helicobacter pylori CagD (HP0545, Cag24) protein is essential for CagA translocation and maximal induction of interleukin-8 secretion.

    abstract::Pathogenic strains of Helicobacter pylori use a type IV secretion system (T4SS) to deliver the toxin CagA into human host cells. The T4SS, along with the toxin itself, is coded into a genomic insert, which is termed the cag pathogenicity island. The cag pathogenicity island contains about 30 open-reading frames, for m...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Cendron L,Couturier M,Angelini A,Barison N,Stein M,Zanotti G

    更新日期:2009-02-13 00:00:00