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[19] Oscillation method with large unit cells

1985; Academic Press; Linguagem: Inglês

10.1016/0076-6879(85)14021-8

1557-7988

Stephen C. Harrison, Fritz K. Winkler, Clarence E. Schutt, Richard Durbin,

Electromagnetic Simulation and Numerical Methods

Background: Simian virus 40 (SV40) and murine polyomavirus (polyoma) are non-enveloped DNA tumor viruses. Their structurally similar capsids, about 500 å in diameter, are formed by 72 pentamers of the major coat protein VP1.Results We describe in this paper the structure determination of SV40 and polyoma at 3.8 å resolution, focusing particularly on methodological issues, and on a comparison of the overall molecular organization in the two related virus particles. Initial phases for SV40 were obtained by single isomorphous replacement at 6.5 å. Phases were refined and the resolution extended to 3.8 å by a combination of strict 5-fold and partial 30-fold electron-density averaging. The structure of polyoma was subsequently determined by systematically translating and rotating the individual VP1 pentamers, in order to find the maximum correlation between calculated and observed structure factors. The resolution was then extended to 3.8 å, also by phase refinement through electron-density averaging.Conclusion The strategies for density averaging and for molecular replacement, used to determine the SV40 and polyoma structures, are likely to be generally useful. The individual building blocks, the VP1 pentamers, are essentially identical in both cases, as are the local details of their interactions with neighboring pentamers. Nevertheless, the arrangement of the pentamers with respect to each other is somewhat different in the two viruses. Whereas SV40 is almost spherical, with all pentamers at identical radii, the pentamers in polyoma that lie on icosahedral fivefold axes are displaced outward by about 5 å.