Large icosahedral capsids contain dedicated stabilizing proteins or multiple protein shells that reinforce one another.
While ordered RNA can be observed, how genomes are condensed and organized within virus particles is largely obscure.
Some large viruses are built with structural elements recognizable from simpler viruses.
Virus particles can contain nonstructural components, including enzymes, small RNAs, and cellular macromolecules.
Figure 4.1 Variation in the size and shape of virus particles. (A) Cryo-electron micrographs of mimivirus and, in the inset (upper left), the parvovirus adeno-associated virus type 4, shown to scale relative to one another to illustrate the ~50-fold range in diameter among viruses that appear roughly spherical. The mimivirus particle (A) is structurally complex: a large number of long, closely packed filaments project from its surface; and one vertex of the capsid carries a unique structure called the stargate, which opens in infected cells to release the viral genome. Rod-shaped viruses also exhibit considerable variation in size, ranging in length from <200 nm to ~2,000 nm. Photos reprinted from Xiao C et al. 2005. J Mol Biol 353:493–496, and Pardon E et al. 2005. J Virol 79:5047–5058, respectively, with permission. Courtesy of Y. Mustafi, National Institutes of Health, and M. Agbandje-McKenna, University of Florida, Gainesville. (B) Nonsymmetric shape of Acidianus bottle-shaped virus isolated from a hot spring in Italy. Adapted from Häring M et al. 2005. J Virol 79:9904–9911, with permission. Courtesy of D. Prangishvili, Institut Pasteur.
Table 4.1 Functions of virion proteins
| Protection of the genome |
| Assembly of a stable protective protein shell |
| Specific recognition and packaging of the nucleic acid genome |
| Interaction with host cell membranes to form the envelope |
| Delivery of the genome |
| Binding to external receptors of the host cell |
| Transmission of signals that induce uncoating of the genome |
| Induction of fusion with host cell membranes |
| Interaction with internal components of the infected cell to direct transport of the genome to the appropriate site |
| Other functions |
| Interactions with cellular components for transport to intracellular sites of assembly |
| Interactions with cellular components to ensure an efficient infectious cycle |
Figure 4.2 Free energy changes in virus particles. Mature virus particles occupy a free energy minimum (1); that is, they are stable, but have not attained the structure with the lowest free energy. Rather, they are primed during assembly and maturation to undergo irreversible conformational transitions (2) that overcome the energy barrier to that lower (more favorable) free energy state (3), and to disassemble at least partially. Such transitions are typically triggered by contact with a host cell receptor or coreceptor or such changes in the environment as a drop in pH. G, free energy; X, reaction coordinate (for example, time after addition of virus particles to susceptible host cells).
As might be anticipated, elucidation of the structures of virus particles and individual structural proteins has illuminated the mechanisms of both assembly of viral nanomachines in the final stages of an infectious cycle and their entry into a new host cell. High-resolution structural information can also facilitate identification of targets for antiviral drugs, as well as the design of such drugs (Volume II, Chapter 8), and provide insights into the dynamic interplay between important viral pathogens and host adaptive immune responses (Volume II, Chapter 4). As we shall see, cataloguing of virus architecture has also revealed completely unanticipated relationships among viruses of different families that infect evolutionarily divergent hosts, and has suggested new principles of virus classification.
Nomenclature
Virus architecture is described in terms of structural units of increasing complexity, from the smallest biochemical unit (the polypeptide chain) to the infectious particle (or virion). These terms, which are used throughout this text, are defined in Table 4.2. Although virus particles are ordered assemblies of macromolecules exquisitely suited for protection and delivery of viral genomes, they are constructed according to the general principles of biochemistry and protein structure.
Methods for Studying Virus Structure
Electron microscopy is the most widely used method for the examination of structure and morphology of virus particles. This technique, which has been applied to viruses since the 1940s, traditionally relied on staining of purified virus particles (or of sections of infected cells) with an electron-dense material. It can yield quite detailed and often beautiful images (Fig. 1.9; see the Appendix) and provided the first rational basis for classification of viruses.
Table 4.2 Nomenclature used in description of virus structure
| Term | Synonym | Definition |
|---|---|---|
| Subunit (protein subunit) | Single, folded polypeptide chain | |
| Structural unit | Asymmetric unit | Unit from which capsids or nucleocapsids are built; may comprise one protein subunit or multiple, different protein subunits |
| Capsid | Coat | The protein shell surrounding the nucleic acid genome |
| Nucleocapsid | Core | The nucleic acid-protein assembly packaged within the virion; used when this assembly is a discrete substructure of a particle |
| Envelope | Viral membrane | The host cell-derived lipid bilayer carrying viral glycoproteins |
| Virion | The infectious virus particle |
The greatest contrast between virus particle and
