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Structure determination of simian virus 40 and murine polyomavirus by a combination of 30-fold and 5-fold
Y Yan1, T Stehle, R C Liddington
1Howard Hughes Medical Institute and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
Background:
Simian virus 40 (SV40) and murine polyomavirus (polyoma) are non-enveloped DNA tumor viruses. Their structurally similar capsids, about 500 degrees 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 degree 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 degree. Phases were refined and the resolution extended to 3.8 degree 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 degree, 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 degree.
Insights
Structural analysis of Simian virus 40 (SV40) and polyomavirus reveals conserved VP1 pentamer building blocks but distinct arrangements, offering insights into viral capsid assembly and related methods.
Area of Science:
- Structural biology
- Virology
- Biophysics
Background:
- Simian virus 40 (SV40) and murine polyomavirus (polyoma) are non-enveloped DNA tumor viruses.
- Their capsids are approximately 500 angstroms in diameter and composed of 72 pentamers of the major coat protein VP1.
Purpose of the Study:
- To determine the high-resolution structures of SV40 and polyoma.
- To compare the molecular organization of these two related viruses.
- To highlight methodological advancements in structure determination.
Main Methods:
- Single isomorphous replacement for initial SV40 phasing.
- Electron-density averaging (5-fold and 30-fold) for phase refinement and resolution extension.
- Molecular replacement by systematic VP1 pentamer translation and rotation for polyoma structure determination.
Main Results:
- SV40 and polyoma structures were determined at 3.8 angstrom resolution.
- VP1 pentamers are structurally conserved and interact similarly in both viruses.
- SV40 exhibits a nearly spherical capsid, while polyoma shows outward displacement of pentamers on fivefold axes.
Conclusions:
- The density averaging and molecular replacement strategies are broadly applicable for viral structure determination.
- Identical VP1 pentamer building blocks and local interactions are observed in both viruses.
- Differences in pentamer arrangement lead to distinct overall capsid morphologies between SV40 and polyoma.