Jasper R. Plaisier

Visualization by Cryo-electron Microscopy of Genomic RNA that Binds to the Protein Capsid Inside Bacteriophage MS2

The icosahedrally symmetrized structure of bacteriophage MS2 as determined by cryo-electron microscopy (EM) reveals the presence of genomic RNA that attaches to coat-protein dimers. Earlier X-ray diffraction studies revealed similar interactions between the unique operator hairpin of the MS2 genomic RNA and the coat-protein dimer. This observation leads us to conclude that not only the operator, but also many other RNA sequences in the genome of MS2, are able to bind to the coat-protein dimer. A substantial number of potential coat-protein-dimer binding sites are present in the genome of MS2 that can account for the observed RNA densities in the EM map. Moreover, it appears that these stem-loop structures are able to bind in a similar fashion to the coat protein dimer as the wild-type operator hairpin. The EM map also shows additional density between the potential operator-binding sites, linking the RNA stem-loops together to form an icosahedral network around the 3 and 5-fold axes. This RNA network is bound to the inside of the MS2 capsid and probably influences both capsid stability and formation, supporting the idea that capsid formation and RNA packaging are intimately linked to each other.

Structures and magnetic properties of Ln3OsO7 (Ln=Pr,Nd,Sm)

Abstract Polycrystalline samples of Ln3OsO7 (Ln=Pr,Nd,Sm) have been prepared. The structures of these compounds were determined by X-ray powder diffraction. They crystallize in a superstructure of cubic fluorite (space group Cmcm, Z=4). The samples have been characterized by magnetometry. The compounds show complex magnetic behavior at low temperatures caused by competing magnetic interactions leading to frustration.

Recycling of aborted ribosomal 50S subunit-nascent chain-tRNA complexes by the heat shock protein Hsp15

When heat shock prematurely dissociates a translating bacterial ribosome, its 50S subunit is prevented from reinitiating protein synthesis by tRNA covalently linked to the unfinished protein chain that remains threaded through the exit tunnel. Hsp15, a highly upregulated bacterial heat shock protein, reactivates such dead-end complexes. Here, we show with cryo-electron microscopy reconstructions and functional assays that Hsp15 translocates the tRNA moiety from the A site to the P site of stalled 50S subunits. By stabilizing the tRNA in the P site, Hsp15 indirectly frees up the A site, allowing a release factor to land there and cleave off the tRNA. Such a release factor must be stop codon independent, suggesting a possible role for a poorly characterized class of putative release factors that are upregulated by cellular stress, lack a codon recognition domain and are conserved in eukaryotes.

Synthesis, structure and luminescence of new Ca3SnSi2O9

Ca3SnSi2O9 was prepared by solid state reaction of CaCO3, SnO2 and SiO2. The crystal structure [a = 732.83(7), b = 1007.43(8), c = 1043.88(9)pm, β = 91.064(2)°, monoclinic, P21c, Z = 4, RP = 2.48, Rwp = 3.27%] has been determined with the Rietveld method from neutron powder diffraction data. The structure has isolated pairs of edge sharing Sn(IV)O6 octahedra. These Sn2O10 groups show an efficient luminescence with a very large Stokes shift.

Area detectors in structural biology

Abstract An overview of area detectors in structural biology is presented. Development of these detectors is one of the main reasons for the exponential rise in the number of structure determinations of large biological complexes. The different techniques used for structure determination put different demands on area detectors. The techniques used in structural biology, X-ray and electron diffraction and electron imaging are discussed and the requirements for a good detector are highlighted. Furthermore, an overview is given of the current state of the art of high-resolution area detectors.

Preparation and crystallographic properties of Sr7−x(Ca/Ba)xMn4O15

Abstract Polycrystalline samples of the new phases Sr7−xAxMn4O15 (A = Ca, Ba; 0 ≤ x ≤ 1) and Sr7−2xCaxBaxMn4O15 (0 ≤ x ≤ 1) have been characterized by X-ray powder diffraction. Apart from changes in the cell parameters, no significant alterations of the crystal structure are found upon doping with Ca and/or Ba. The application of chemical pressure causes an anisotropic change of the unit cell with the a (Ca) and b (Ba) axes showing the largest changes. The compounds with double-doping Sr7−2xCaxBaxMn4O15 show a more complicated behavior. The cell volume is linear dependent on the average ionic radius of the A-cation, for all compounds. Ca enters the structure on the small Sr(1) site, whereas Ba occupies the larger Sr(3) and Sr(4) sites. The results show that the structure of Sr7Mn4O15 is flexible with respect to the average size of the A-cation.

Structure determination of a new apatite: Ba5OsO5)3Cl

The crystal structure of Ba5(OsO5)3Cl is described. Ba5(OsO5)3Cl, MT = 1395.3, hexagonal, P63cm, a = 10.928(2) A, c = 7.824(5) A, V = 809.2(6) A3, Dx =6.290 Mg/m3. λ(MoKα) = 0.71069A, F(000) = 1170, room temperature, final R = 0.051 for 2900 observed reflections. The structure is isomorphous with Ba5(ReO5)3Cl and is similar to that of standard chlorapatite; the PO4 tetrahedra are replaced by pyramidal OsO5 groups.

Structure determination of Ba4Os6O18Cl

The crystal structure of Ba4Os6O18Cl is described. Ba4Os6O18Cl, Mr = 2013.97, cubic, I23, a = 9.380(1) A, V = 825.3(3) A3, Z = 2, Dx = 8.104 Mg/m3, λ(MoKα) = 0.71069 A, F(000) = 1538, room temperature, final Rw = 0.019 for 203 observed Friedel pairs. The structure is related to that of KSbO3 and is similar to that of La4Os6O19. The La4O groups are replaced by Ba4Cl groups.

Synthesis and structure of Ba5(OsO5)3NO3

Abstract The crystal structure of Ba 5 (OsO 5 ) 3 NO 3 is described. It crystallizes in an apatite-like structure, space group P6 3 cm, a = 11.101(1) A, c = 7.815(1) A, V = 834.0(2) A 3 , Z = 2, P calc = 6.208 Mg·m −3 . The structure is isomorphous with Ba 5 (OsO 5 ) 3 Cl and Ba 5 (ReO 5 ) 3 NO 3 .

A contribution to the understanding of phase equilibria [structure of Sr7ZrSi6O21]

The crystal structure of Sr[sub 7]ZrSi[sub 6]O[sub 21] is described. Sr[sub 7]ZrSi[sub 6]O[sub 21], M[sub r] = 1,209.10, triclinic, P[bar 1], a = 8.398(3)[angstrom], b = 8.435(2)[angstrom], c = 8.445(3)[angstrom], [alpha] = 106.13(3)[degree], [beta] = 106.49(3)[degree], [gamma] = 105.90(3)[degree], V = 509.0(3)[angstrom][sup 3], Z = 1, D[sub x] = 3.944(3) Mgr/m[sup 3]. [gamma](MoK[alpha]) = 0.71069[angstrom], F(000) = 558, room temperature, final R = 0.073 for 1,145 observed reflections. The structure is pseudo rhombohedral, R[bar 3], a[sub hex] = 13.474[angstrom], c[sub hex] = 9.714[angstrom], Z = 3. The crystal structure determination establishes the formula for the compound earlier described in phase equilibria studies as Sr[sub 6]ZrSi[sub 5]O[sub 18].