13 and 5).
The tegument contains >20 viral proteins, viral RNAs, and cellular components. A few tegument proteins are icosahedrally ordered, as a result of direct contacts with the structural units of the capsid. For example, three tegument proteins form a distinctive structure that caps the pentons and buttresses their association with neighboring triplexes. Tegument proteins are not uniformly distributed around the capsid, but are concentrated on one side, where they form a well-defined cap-like structure (Fig. 4.27A). The connection of the portal vertex of the capsid to the viral membrane (Fig. 4.27D) seems likely to account for this asymmetry.
Mimiviruses
Characteristic features of members of the Mimiviridae, which infect single-cell eukaryotes, are their very large, double-stranded DNA genomes and correspondingly huge particles. Initial examinations of these viruses by electron microscopy established that they comprise multiple layers, include a lipid membrane within an external capsid, and in some cases include a dense layer of surface fibers (Fig. 4.1). Despite their large size, mimivirus particles exhibit some familiar structural features, notably icosahedral symmetry and a capsid built from a major capsid protein with the double β-barrel jelly roll topology. To date, cryo-EM reconstructions of these viruses have achieved only a relatively low resolution, because of the need for much computational power (e.g., ~3 × 106 CPU hours for a 21-Å view of Cafeteria roenbergensis virus) and/or removal of dense surface fibers (as for a 65-Å reconstruction of Acanthamoeba polyphaga mimivirus). Such studies have revealed the icosahedral organization of major capsid proteins (Fig. 4.28) and in some cases their arrangement into assemblies that interact around the five- or threefold axes of symmetry. The most unique feature, first observed in Acanthamoeba polyphaga mimivirus, is the presence of a star-shaped structure at one vertex (Fig 4.28B). This stargate, which allows release of internal contents of virus particles into the cytoplasm of infected cells, is an exceptionally large vertex structure, with arms extending almost to neighboring vertices. As yet, little is known about how such large capsids (up to ~5,000 Å in diameter) are stabilized, or the organization of their internal components.
Figure 4.27 Structural features of herpesvirus particles. (A) Two slices through a cryo-electron tomogram of a single herpes simplex virus type 1 particle, showing the eccentric tegument cap (arrowheads). Reprinted from Grunewald K et al. 2003. Science 302:1396–1398, with permission. (B) Diagram of the structure of the herpesviral capsid based on high resolution (3.5 Å or better) cryo-EM structures of herpes simplex virus 1 and 2 and illustrated within a virus particle. Shown below is an enlarged view down a 5-fold axis of icosahedral symmetry. (C) The single portal of herpes simplex virus type 1 nucleocapsids visualized by staining with an antibody specific for the viral UL6 protein conjugated to gold beads is shown to the left. The gold beads are electron dense and appear as dark spots in the electron micrograph. They are present at a single vertex in each nucleocapsid, which therefore contains one portal. A 16-Å reconstruction of the UL6 protein portal based on cryo-EM is shown on the right. Adapted from Trus BL et al. 2004. J Virol 78:12668–12671, with permission. (D) Central slice through a cryo-electron tomographic reconstruction based on symmetryfree averaging is shown radially colored as indicated. Portal vertex-associated density is shown in cyan and purple. Adapted from Schmid MF et al. 2012. PLoS Pathog 8:e1002961, under license CC BY 4.0. © Schmid et al. Courtesy of A.C. Steven, National Institutes of Health (A and C), W. Chiu, Baylor College of Medicine (B), and F.J. Rixon, MRC-University of Glasgow Center for Virus Research, Glasgow, United Kingdom (D).
Alternative Architectures
The particles of other large viruses exhibit regular and sometimes remarkable morphologies that are not obviously based on helical or icosahedral symmetry. One example, Acidianus bottle-shaped virus, is portrayed in Fig. 4.1. We briefly describe two others here to illustrate the structural diversity of such viruses.
Poxviruses
Particles of poxviruses such as vaccinia virus also comprise multiple, distinct structural elements, but none of these exhibit obvious icosahedral or helical symmetry. A second distinctive feature is that two forms of infectious particles are produced in vaccinia virus-infected cells (see Chapter 13), termed mature virions and enveloped extracellular virions, which differ in the number and origin of membranes. Mature virions are large, enveloped structures (~350 to 370 × 250 × 270 nm) comprising at least 75 proteins that appear in the electron microscope as brick or barrel shaped (depending on the orientation) (Fig. 4.29A). A number of internal structures have been observed by examination of thin sections through purified particles or by cryo-electron tomography (Fig. 4.29B). These features include the core wall, which surrounds the central core that contains the ~200-kbp DNA genome, and lateral bodies. Remarkably, the core contains some 20 enzymes with many different activities. Although viral proteins that contribute to these various structures have been identified, our understanding of vaccinia virus architecture remains at low resolution.
Figure 4.28 Features of mimivirus capsids. (A) Cryo-EM reconstruction of Cafeteria roenbergensis mimivirus at 21-Å resolution. Although not decorated with fibers, the surface of this capsid is characterized by high protrusions formed by surface loops of the double β-barrel jelly roll major capsid protein. These pseudohexagonal structure units are organized in discrete arrays, termed pentasymmetrons (purple) and trisymmetrons (blue, red, green, cyan, and orange), which form the vertices and interact at the threefold axes of symmetry, respectively. One of the 30 edges of the icosahedral particle is indicated in cyan, and the position of five-, three-, and twofold axes of symmetry by red symbols. Adapted from Xiao C et al. 2017. Sci Rep 7:5484, under license CC BY 4.0. Courtesy of C. Xiao, University of Texas at El Paso. (B) Cryo-EM reconstruction of Acanthamoeba polyphaga mimivirus following sequential digestion with lysozyme and the protease bromelain. This treatment was applied to remove (or reduce) the dense array of surface fibers (Fig. 4.1), which increase ice thickness around the particles and hence signal-to-noise because of random scattering of electrons. The reconstruction (61 Å), which is based on only fivefold averaging, is viewed down the stargate (blue). The size of this assembly with extensions of the arms some 200 Å almost to neighboring vertices is clearly evident. Adapted from Xiao C et al. 2009. PLoS Biol 7:e92 under license CC BY 4.0. © 2009 Xiao et al. Courtesy of M. Rossman, Purdue University.
Pithoviruses
Pithovirus particles are the largest described to date, indeed are visible in the light microscope. They are ovoid or amphora-like in shape and variable in length (most commonly 1.35 to 1.65 nm). The internal
