Structural studies of the Sputnik virophage

Abstract

The virophage Sputnik is a satellite virus of the giant mimivirus and is the only satellite virus reported to date whose propagation adversely affects its host virus' production. Genome sequence analysis showed that Sputnik has genes related to viruses infecting all three domains of life. Here, we report structural studies of Sputnik, which show that it is about 740 A in diameter, has a T=27 icosahedral capsid, and has a lipid membrane inside the protein shell. Structural analyses suggest that the major capsid protein of Sputnik is likely to have a double jelly-roll fold, although sequence alignments do not show any detectable similarity with other viral double jelly-roll capsid proteins. Hence, the origin of Sputnik's capsid might have been derived from other viruses prior to its association with mimivirus.

FIG. 1.

Micrograph of Sputnik particles embedded in vitreous ice, recorded using a Philips CM200 FEG electron microscope.

FIG. 2.

CryoEM reconstruction of Sputnik at 10.7-Å resolution. (A) Shaded-surface representation of the Sputnik 3D density map viewed along an icosahedral 2-fold axis. The white triangle marks the boundary of an icosahedral asymmetric unit. The numbers show the positions of icosahedral 2-, 3-, and 5-fold axes limiting an asymmetric unit. (B) Radial sections of the cryoEM map at different radii, with gray scale used to denote density levels, with white being the highest density.

FIG. 3.

Cross-section through the Sputnik cryoEM map. The orientation of the icosahedral (2-, 3-, and 5-fold) axes is shown with white lines. Note the probable lipid bilayer under the protein capsid and the “mushroom”-like fibers on the trimeric capsomers. In the zoomed view, a black arrow is pointing toward possible transmembrane protein densities.

FIG. 4.

Structure of PBCV-1 Vp54 fitted into the Sputnik cryoEM density. (A) Shaded-surface representation of the Sputnik 3D density map viewed along an icosahedral 2-fold axis. The fitted Vp54 structures are shown as ribbons. Symmetry-related capsomers are shown in the same color. The capsomers counted along the h and k axes demonstrate T=27 quasisymmetry. (B, bottom) Central sliced view of half of the Sputnik 3D map fitted with Vp54. (Top) A zoomed view of one of the capsomers is shown as a stereo pair. The position of Ala 291 shows that the uninterpreted density corresponds to an insertion in the DE loop of PBCV-1 Vp54.