subunits of viral protein – often termed a capsomer. The capsid functions to provide a protein shell in which the chemically labile viral genome can be maintained in a stable environment. The association of capsids with genomes is a complex process, but it must result in an energetically stable structure. While viruses can assume a range of shapes, some quite complex, given the dimensions of virus structure and the constraints of the capsomer's structural parameters, a very large number assume one of two regular shapes. The first is the helix, in which the capsomers associate with helical nucleic acid as a nucleoprotein – these can be either stiff or flexible depending upon the properties of the capsid proteins themselves. The other highly regular shape is the icosahedron, in which the capsomers form a regular solid structure enfolding the viral genome. Despite the frequency of such regular shapes, many viruses have more complex and/or less regular appearances; these include spindle, kidney, lemon, and lozenge shapes. Further, some viruses can assume different shapes depending upon the nature of the cells in which they mature, and some groups of viruses – notably the poxviruses – are distinguished by having a number of different shapes characterizing specific members of the group. Arrangement of the capsid around its viral genetic material is unique for each type of virus. The general properties of this arrangement define the shape of the capsid and its symmetry, and since each type of virus has a unique shape and structural arrangement based upon the precise nature of the capsids proteins and how they interact, capsid shape is a fundamental criterion in the classification of viruses.
The technique of x‐ray crystallography has been applied fruitfully to the study of capsid structures of some smaller icosahedral viruses, and structural solutions for human rhinovirus, poliovirus, foot and mouth disease virus, and canine parvovirus are available. In addition, the structures of a number of plant viruses have been determined. Since the method requires the ability to crystallize the subject material, it is not certain that it can be directly applied to larger, more complex viruses. Still, the structures of specific protein components of some viruses – such as the membrane‐associated hemagglutinin of influenza virus – have been determined.
The x‐ray crystallographic structure of Desmodium yellow mottle virus – a pathogen of beans – is shown in Figure 5.3, to illustrate the basic features of icosahedral symmetry. The icosahedral shell has a shape similar to a soccer ball, and the 12 vertices of this regular solid are arranged in a relatively simple pattern at centers of fivefold axes of symmetry. Each edge of the solid contains a twofold axis of symmetry, and the center of each of the 20 faces of the solid defines a threefold axis of symmetry. While a solid icosahedron can be visualized as composed of folded sheets, the virion structure is made up of repeating protein capsomers that are arrayed to fit the symmetry's requirements. It is important to see that the peptide chains themselves have their own distinct morphology, and it is their arrangement that makes up individual capsomers. The overall capsid structure reflects the next level of structure. Morphology of the individual capsomers can be ignored without altering the basic pattern of their arrangement. Further detail is shown in Figure 5.4, where the assembly of the single capsomer protein into two subunits of the capsid, a penton or a hexon, is shown.
Twelve pentons and 20 hexons assemble to form the capsid itself. The core of the capsid is filled with the viral genome, in this case RNA. This RNA is also arranged very precisely, with the bulk forming helical stretches and the regions coming in close contact with the inner surface of the capsid shell, forming open loops.
Viral envelopes
A naked capsid defines the outer extent of bacterial, plant, and many animal viruses, but other types of viruses have a more complex structure in which the capsid is surrounded by a lipid envelope. This envelope is made up of a lipid bilayer that is derived from the cell in which the virus replicates and from virus‐encoded membrane‐associated proteins. The presence or absence of a lipid envelope (described as enveloped or naked, respectively) is another important defining property of different groups of animal viruses.
Figure 5.3 Crystallographic structure of a simple icosahedral virus. (a) The structure of Desmodium yellow mottle virus as determined by x‐ray crystallography to 2.7‐Å resolution. This virus is a member of the tymovirus group and consists of a single positive‐strand RNA genome about 6300 nucleotides long. The virion is 25–30 nm in diameter and is made up of 180 copies of a single capsid protein that self‐associates in two basic ways: in groups of 5 to form the 12 pentons, and in groups of six to form the 20 hexamers. Two views are shown: Panels at left are looking down at a fivefold axis of symmetry, and the right‐hand panels look at the threefold and twofold axes. Note that the individual capsomers arrange themselves in groups of five at vertices of the icosahedra, and in groups of six on the icosahedral faces. Since there are 12 vertices and 20 faces, this yields the 180 capsomers that make up the structure. The axes are outlined in the lower panels.
Source: Courtesy of S. Larson and A. McPherson, University of California, Irvine.
(b) Schematic diagram of the vertices and faces of a regular icosahedron showing the axes of symmetry. Arrangements of the capsomers described in (a) are also shown.
Figure 5.4 The structure of a simple icosahedral virus. (a) A space‐filling model of the capsid of Desmodium yellow mottle virus as determined by x‐ray crystallography to 2.7‐Å resolution. (b) The assembly of the single capsid protein into 12 pentons and 20 hexons to form the capsid.
Source: Courtesy of S. Larson and A. McPherson, University of California, Irvine.
(c) The structure of the RNA genome inside the capsid as determined by x‐ray crystallography.
The shape of a given type of virus is determined by the shape of the virus capsid and really does not depend on whether or not the virus is enveloped. This is because for most viruses, the lipid envelope is amorphous and deforms readily upon preparation for visualization using the electron microscope.
CLASSIFICATION SCHEMES
As we have noted, since it is not clear that all viruses have a common origin, a true Linnaean classification is not possible, but a logical classification is invaluable for understanding the detailed properties of individual viruses and how to generalize them. Schemes dependent on basic properties of the virus, as well as specific features of their replication cycle, afford a useful set of parameters for keeping track of the many different types of viruses. A good strategy for remembering the basics of virus classification is to keep track of the following:
1 What kind of genome is in the capsid: Is it DNA or RNA? Is it single stranded or double stranded? Is the genome circular or linear, composed of a single piece or segmented?
2 How is the protein arranged around the nucleic acid; that is, what are the symmetry and dimensions of the viral capsid?
3 Are there other components of the virion?Is there an envelope?Are there enzymes in the virion required for initiation of infection or maturation of the virion?
Note that this very basic scheme does not ask what type of cell the virus infects. There are clear similarities between some viruses whether they infect plants, animals, or bacteria. Despite this, however, it is clear that basic molecular processes are
