Section 19.5.8.4. Helical viruses and bacteriophages

The largest repeating units in structures determined by fibre diffraction are those of several members of the tobamovirus family, including tobacco mosaic virus (Namba et al., 1989), cucumber green mottle mosaic virus (Wang & Stubbs, 1994) and ribgrass mosaic virus (Wang et al., 1997). These viruses are rod-shaped, 3000 Å long and about 180 Å in diameter. Oriented sols yield exceptionally good diffraction patterns (Fig. 19.5.8.1). The asymmetric unit consists of a protein subunit of approximate molecular weight 18 000 Da and three nucleotides of RNA. The coat proteins are folded like globular proteins and are about 40% α-helical, with small regions of β-sheet. All of the amino acids, all three nucleotides, and in some cases water molecules and calcium ions, are seen in the electron-density maps. The TMV structure was determined by MDIR; the remaining structures were determined by molecular replacement from TMV or by a combination of molecular replacement and isomorphous replacement. All of the structures were refined by restrained least-squares or molecular-dynamics methods to R values of less than 0.10 at resolutions between 2.9 and 3.5 Å.

Figure 19.5.8.1| top | pdf | X-ray diffraction pattern from an oriented sol of the U2 strain of tobacco mosaic virus.

Several filamentous bacteriophage structures, including fd, Pf1 and related strains, have been determined and refined. Filamentous bacteriophages are flexible viruses, about 60 Å in diameter and 10 000 to 20 000 Å in length. Several thousand copies of a coat protein of about 50 residues wrap around a central single-stranded circular DNA. The DNA does not appear to be sufficiently ordered to appear in electron-density maps. The coat-protein molecules have an unusually simple structure, being almost entirely α-helical (Marvin et al., 1974). Model-building approaches have therefore been used, sometimes supplemented by isomorphous replacement (Bryan et al., 1983). Neutron scattering from bacteriophages with selectively deuterated amino-acid residues has also been used to assist model building (Nambudripad et al., 1991). Both restrained least-squares (Nambudripad et al., 1991) and molecular-dynamics (Gonzalez et al., 1995) refinement methods have been used. Although there is not complete agreement about the structure, the coat protein clearly forms two α-helical layers, possibly with a short intervening peptide loop (Nambudripad et al., 1991).