Structure of flexible filamentous plant viruses

Abstract

Flexible filamentous viruses make up a large fraction of the known plant viruses, but in comparison with those of other viruses, very little is known about their structures. We have used fiber diffraction, cryo-electron microscopy, and scanning transmission electron microscopy to determine the symmetry of a potyvirus, soybean mosaic virus; to confirm the symmetry of a potexvirus, potato virus X; and to determine the low-resolution structures of both viruses. We conclude that these viruses and, by implication, most or all flexible filamentous plant viruses share a common coat protein fold and helical symmetry, with slightly less than 9 subunits per helical turn.

FIG. 1.

Example of a calculated diffraction pattern from a segment of SMV in a cryo-electron micrograph. The arrow indicates the first intensity peak in the first layer line. The position of this layer line corresponds to a spacing of about 165 Å; near-meridional layer lines corresponding to a spacing of 33 Å are also clearly visible. For phases to be used in symmetry determination, the first-layer-line intensities in the four quadrants were required to be clearly visible and symmetric in position and appearance.

FIG. 2.

(A) and (B) Wide-angle fiber diffraction patterns from the potyvirus SMV (A) and the potexvirus NMV (B), with intensities corrected and data transformed into reciprocal space. The arrow in panel A indicates the first layer line. (C) Low-angle data from SMV, corrected and transformed.

FIG. 3.

SDS-PAGE from SMV. Two bands from degradation products of SMV coat protein are clearly visible.

FIG. 4.

Radial density distribution in SMV. Units of electron density (ρ) are arbitrary.

FIG. 5.

Convergence of the rotation angle ϕ as a function of cycle number during IHRSR. Refinements were started from many different rotation angles; provided that the angle was not too far from the final refined angle (21), they all converged to the same value. Most of the refinements used solid cylinders as initial reference volumes, but for SMV, arbitrary unrelated density distributions (solid inverted triangles, open diamonds, and solid diamonds) were also used.

FIG. 6.

Fourier shell correlation plots for the refined PVX and SMV models. In both cases, the correlations fall below 0.5 at a resolution of about 1/14 Å.

FIG. 7.

(A) Cryo-electron micrograph of SMV with contrast reversed. Scale bar, 250 Å. (B) IHRSR reconstruction of SMV, section normal to viral axis. Scale bar (also applies to panels C and D), 50 Å. (C) IHRSR reconstruction of SMV, outside surface view. (D) IHRSR reconstruction of SMV, section through viral axis. (E) Cryo-electron micrograph of PVX with contrast reversed. Scale bar, 250 Å. (F) IHRSR reconstruction of PVX, section normal to viral axis. Scale bar (also applies to panels G and H), 50 Å. (G) IHRSR reconstruction of PVX, outside surface view. (H) IHRSR reconstruction of PVX, section through viral axis. Color coding in panels B, C, D, F, G, and H is from red-orange (low density) to green-blue (high density).