Icosahedral Symmetry - Viruses And Human Disease

TABLE 2.1

Listing of Selected Vertebrate Virus Families by Morphology

Morphology

Triangulation

Morphology

of particle/virus family

Enveloped

number

of nucleocapsid

Figure numbers

Icosahedral

Adenoviridae

T = 25

Not applicable

Figs. 2.1, 2.12

T = 13l a

Reoviridae

Icosahedral

Figs. 2.1, 2.5, 2.11

P = 7d a,b

Figs. 2.1,c 2.5

Papillomaviridae

Not applicable

P = 7d a,b

Figs. 2.1,c 2.5, 2.10

Polyomaviridae

Not applicable

Parvoviridor

T=1

Not applicable

Figs. 2.1, 2.5

Figs. 2.1,d 2.5, 2.7, 2.8

P = 3b

Picornaviridae

Not applicable

Astroviridae

Not applicable

Caliciviridae

T=3

Not applicable

Herpesviridae

Yes

T = 16

Icosahedral

Figs. 2.1, 2.5, 2.20

Togaviridae

Yes

T=4

Icosahedral

Figs. 2.5, 2.14, 2.18

Flaviviridae

Yes

T=3

Icosahedral

Figs. 2.5, 2.18

Irregular

Poxviridae (ovoid)

Yes

Dumbbell

Figs. 2.1, 2.24

Rhabdoviridae (bacilliform)

Yes

Coiled helix

Figs. 2.1, 2.23

Spherical

Retroviridae

Yes

Icosahedral?

Figs. 2.1, 2.21

Rounde

Coronaviridae

Yes

Helical or tubular

Paramyxoviridae

Yes

Helical

Fig. 2.22

Orthomyxoviridae

Yes

Helical

Figs. 2.1, 2.22

Bunyaviridae

Yes

Helical

Arenaviridae

Yes

Helical

Hepadnaviridae

Yes

T=3&4

Icosahedral

Filamentousc

Filoviridae

Yes

Helical

Fig. 2.19

Two mirror image structures can be formed using T = 13 or T = 7, a symmetry referred to as "d" or "l."

Because the subunits are not exactly equivalent, Papillomaviridae, Polyomaviridae, as well as poliovirus, have "pseudo-triangulation numbers" so are

referred to as P = 7, P = 7, and P = 3 symmetries respectively.

Papovaviridae, referred to in Fig. 2.1 have now been separated into Polyomaviridae and Papillomaviridae.

Enterovirus, referred to in Fig. 2.1 is a genus of the Picornaviridae.

Virions are often pleiomorphic.

ICOSAHEDRAL SYMMETRY

edge possesses twofold rotational symmetry. Thus the

icosahedron is characterized by twofold, threefold, and five-

fold symmetry axes. The dodecahedron, the next simpler

Virions can be approximately spherical in shape, based

regular solid, has the same symmetry axes as the icosahe-

on icosahedral symmetry. Since the time of Euclid, there

dron and is therefore isomorphous with it in symmetry: the

have been known to exist only five regular solids in which

dodecahedron has 12 faces which are regular pentagons, 20

each face of the solid is a regular polygon: the tetrahedron,

vertices where three faces meet, and 30 edges with twofold

the cube, the octahedron, the dodecahedron, and the icosa-

symmetry. The three remaining regular solids have differ-

hedron. The icosahedron has 20 faces, each of which is a

ent symmetry axes. The vast majority of regular viruses that

regular triangle, and thus each face has threefold rotational

appear spherical have icosahedral symmetry.

symmetry (Fig. 2.3A). There are 12 vertices where 5 faces

In an icosahedron, the smallest number of subunits that

meet, and thus each vertex has fivefold rotational symme-

can form the three-dimensional structure is 60 (5 subunits at

try. There are 30 edges in which 2 faces meet, and each

POX-

HERPES-

ADENO-

PAPOVA-

PARVO-

MYXO-

RETRO-

RHABDO-

REO-

ENTERO-

FIGURE 2.1 Relative sizes and shapes of representative (A) DNA- and (B) RNA- containing viruses. In each panel the

top row shows negatively stained virus preparations, the second row shows thin sections of virus-infected cells, and the

bottom row illustrates schematic diagrams of the viruses. Magnification of the electron micrographs is 50,000. From

Granoff and Webster (1999), p. 401.

RNA

100 nm

FIGURE 2.2 Structure of TMV, a helical plant virus. (A) Schematic diagram of a TMV particle showing about 5%

of the total length. From Murphy et al. (1995), p. 434. (B) Electron micrograph of a negatively stained TMV rod. From

www.ncbi.nlm.nih.gov.

HOOC

GD I B

FIGURE 2.3 A simple icosahedral virus. (A) Diagram of an icosahedral capsid made up of 60 identical copies of

a protein subunit, shown as blue trapezoids labeled "A." The twofold, threefold, and fivefold axes of symmetry are

shown in yellow. This is the largest assembly in which every subunit is in an identical environment. (B) Schematic

representation of the subunit building block found in many RNA viruses, known as the eightfold β barrel or β sandwich.

The β sheets, labeled B through I from the N terminus of the protein, are shown as yellow and red arrows; two possible

α helices joining these sheets are shown in green. Some proteins have insertions in the CD, EF, and GH loops, but

insertions are uncommon at the narrow end of the wedge (at the fivefold axis). From Granoff and Webster (1999) Vol. 3,

color plate 31. [Originally from J. Johnson (1996)].

each of the 12 vertices, or viewed slightly differently, 3 units

1, 3, 4, 7, 9, 12, 13, 16, and so forth. A subunit defined in

on each of the 20 triangular faces). Some viruses do in fact

this way is not necessarily formed by one protein molecule,

use 60 subunits, but most use more subunits in order to pro-

although in most cases this is how a structural subunit is in

vide a larger shell capable of holding more nucleic acid.

fact formed. Some viruses that form regular structures that

The number of subunits in an icosahedral structure is 60T,

are constructed using icosahedral symmetry principles do

where the permissible values of T are given by T = H 2 +

not possess true icosahedral symmetry. In such cases they

HK + K 2, where H and K are integers and T is called the

are said to have pseudo-triangulation numbers. Examples

triangulation number. Permissible triangulation numbers are

are described later.

Structural studies of viruses have shown that the cap-

Because the size of the icosahedral shell is fixed by

sid proteins that form the virions of many plant and animal

geometric constraints, it is difficult for a change in the size

icosahedral viruses have a common fold. This fold, an eight-

of a viral genome to occur. A change in size will require a

stranded antiparallel β sandwich, is illustrated in Fig. 2.3B.

change in the triangulation number or changes in the cap-

The presence of a common fold suggests that these capsid

sid proteins sufficient to produce a larger or smaller internal

proteins have a common origin even if no sequence identity is

volume. In either case, the changes in the capsid proteins

detectable. The divergence in sequence while maintaining this

required are relatively slow to occur on an evolutionary

basic fold is illustrated in Fig. 2.4, where capsid proteins of

timescale and the size of an icosahedral virus is "frozen" for

three viruses are shown. SV40 (family Polyomaviridae), polio-

long periods of evolutionary time. For this reason, as well as

virus (family Picornaviridae), and bluetongue virus (family

for other reasons, most viruses have optimized the informa-

Reoviridae) are a DNA virus, a single-strand RNA virus, and

tion content in their genomes, as will be clear when indi-

a double-strand RNA virus, respectively. Their capsid pro-

vidual viruses are discussed in the following chapters.

teins have insertions into the basic eight-stranded antiparallel

β-sandwich structure that serve important functions in virus

Comparison of Icosahedral Viruses

assembly. However, they all possess a region exhibiting the

common β-sandwich fold and may have originated from a

Cryoelectron microscopy has been used to determine the

common ancestral protein. Thus, once a suitable capsid protein

structure of numerous icosahedral viruses to a resolution of

arose that could be used to construct simple icosahedral parti-

7 to 25 Å. For this, a virus-containing solution on an electron

cles, it may ultimately have been acquired by many viruses.

microscope grid is frozen very rapidly so that the sample

The viruses that possess capsid proteins with this fold may be

is embedded in amorphous frozen water. The sample must

related by descent from common ancestral viruses, or recombi-

be maintained at liquid nitrogen temperatures so that ice

nation may have resulted in the incorporation of this successful

crystals do not form and interfere with imaging. Unstained,

ancestral capsid protein into many lines of viruses.

slightly out-of-focus images of the virus are captured on

C(361)

C(238)

N(1)

N(15)

SV40 VP1 P = 7

Poliovirus1 VP3 P = 3

C(349)

N(1)

Bluetongue virus VP7 T = 13

FIGURE 2.4

Structure of three vertebrate virus protein subunits that assemble into icosahedral shells. The N termini

and C termini are labeled with the residue number in parenthesis. The β barrels are shown as red arrows, α helices are

gray coils, and the subunit regions involved in quasi-symmetric interactions that are critical for assembly are colored

green. SV40 and PV have triangulation numbers of "pseudo-T=7" or P = 7 and "pseudo-T=3" or P = 3, respectively.

Adapted from Granoff and Webster (1999), Vol. 3, plate 32.

film, or more recently captured electronically, using a low

which is 1250 Å in diameter and has T=16 symmetry (the

dose of electrons. These images are digitized and the den-

virion is enveloped but only the nucleocapsid is regular).

sity measured. Mathematical algorithms that take advantage

The rotavirus and reovirus virions are smaller and have

of the symmetry of the particle are used to reconstruct the

T=13. Human papillomavirus and mouse polyomavirus are

structure of the particle.

pseudo-T=7. Ross River virus (RRV) (family Togaviridae)

A gallery of structures of viruses determined by cryoelec-

is enveloped but has regular symmetry, with T=4. Several

tron microscopy is shown in Fig. 2.5. All of the images are to

examples of viruses with T=3 or pseudo-T=3 are shown

scale so that the relative sizes of the virions are apparent. The

(dengue 2, flock house, rhino-, polio-, and cowpea mosaic

largest particle is the nucleocapsid of herpes simplex virus,

viruses, of which dengue 2 is enveloped but regular and the

Rotavirus

(1000 Å)

Herpes Simplex

500 Å

(1250 Å)

Ross River (700 Å)

Reovirus (Lang)

(850 Å)

Dengue 2 (490 Å)

Human papilloma (600 Å)

Polyoma (495 Å)

Flockhouse Human rhinovirus

Poliovirus Cowpea mosaic

B19 parvovirus

(330 Å)

(320 Å)

(312 Å)

(260 Å)

FIGURE 2.5 Gallery of three-dimensional reconstructions of icosahedral viruses from cryoelectron micrographs. All

virus structures are surface shaded and are viewed along a twofold axis of symmetry except Ross River, which is viewed

along a three-fold axis. All of the images are of intact virus particles except for the herpes simplex structure, which is of

the nucleocapsid of the virus. Most of the images are taken from Baker et al. (1999), except the images of Ross River

virus and of dengue virus, which were kindly provided by Drs. R. J. Kuhn and T. S. Baker.

construct the shell. The structures of two insect viruses

rest are not enveloped). B19 parvovirus has T=1. The gen-

that are also simple T=3 structures have also been solved.

eral correlation is that larger particles are constructed using

As an example of these simple structures, the T=3 capsid

higher triangulation numbers, which allows the use of larger

of the insect virus, flock house virus (family Nodaviridae),

numbers of protein subunits. Larger particles accommodate

is illustrated in Fig. 2.6.

larger genomes.

The 180 subunits in these T=3 structures interact with one

another in one of two different ways, such that the protein

Atomic Structure of T=3 Viruses

shell can be thought of as being composed of an assembly

of 60 AB dimers and 30 CC dimers (Fig. 2.6A). The bond

Because the simplest viruses are regular structures, they

angle between the two subunits of the dimer is more acute

will often crystallize, and such crystals may be suitable for

in the AB dimers than in the CC dimers (Figs. 2.6B and C).

X-ray diffraction. Many viruses formed using icosahedral

For the plant viruses, there are N-terminal and C-terminal

symmetry principles have been solved to atomic resolu-

extensions from the capsid proteins that are involved in

tion, and a discussion of representative viruses that illus-

interactions between the subunits and with the RNA. The

trate the principles used in construction of various viruses

N-terminal extensions have a positively charged, disordered

is presented here.

domain for interacting with and neutralizing the charge on

Among T=3 viruses, the structures of several plant

the RNA and a connecting arm that interacts with other

viruses, including tomato bushy stunt virus (TBSV) (genus

subunits. In the case of the CC dimers, the connecting arms

Tombusvirus, family Tombusviridae), turnip crinkle virus

interdigitate with two others around the icosahedral three-

(TCV) (genus Carmovirus, family Tombusviridae), and

fold axis to form an interconnected internal framework. In

Southern bean mosaic virus (SBMV) (genus Sobemovirus,

the case of the AB conformational dimer, the arms are dis-

not yet assigned to family), have been solved. All three

ordered, allowing sharper curvature. For flock house virus,

of these viruses have capsid proteins possessing the

eight-stranded antiparallel β sandwich. T=3 means that

the RNA plays a role in controlling the curvature of the CC

dimers, as illustrated in Fig. 2.6.

180 identical molecules of capsid protein are utilized to

dsRNA

Arm

dsRNA

FIGURE 2.6 (A) Diagrammatic representation of a T=3 virus, flock house virus. The positions of the three identical

proteins that make up a triangular face are only quasi-equivalent. The angle between the A and B5 units (shown with a

red oval and in diagram (C) is more acute than that along the CC2 edge, shown with a blue oval, and diagram (B). This

difference in the angles is due to the presence of an RNA molecule located under the CC2 edge. From Johnson (1996),

with permission.

Atomic Structure of Viruses Having

Pseudo-T=3 Symmetry

The structures of several picornaviruses and of a plant

comovirus (cowpea mosaic virus) have also been solved to

atomic resolution. The structures of these viruses are simi-

lar to those of the plant T=3 viruses, but the 180 subunits

that form the virion are not all identical. A comparison of

the structure of a T=3 virus with those of poliovirus and of

cowpea mosaic virus is shown in Fig. 2.7. Poliovirus has

60 copies of each of three different proteins, whereas the

comovirus has 60 copies of an L protein (each of which

fills the niche of two units) and 60 copies of an S protein.

All three poliovirus capsid proteins have the eight-stranded

antiparallel β-sandwich fold. In the comoviruses, the L pro-

tein has two β-sandwich structures fused to form one large

protein, and the S protein is formed from one sandwich.

The structures of the picornavirus and comovirus virions

are called pseudo-T=3 or P=3, since they are not true T=3

structures.

The picornavirus virion is 300 Å in diameter. The 60 mol-

ecules of each of the three different proteins have different

roles in the final structure, as illustrated in Fig. 2.8, in which

FIGURE 2.8

Three-dimensional space-filling model of the human

the structure of a rhinovirus is shown. Notice that five copies

rhinovirus 14 virion, based upon X-ray crystallographic data. VP1 is shown

in blue, VP2 in green, and VP3 in red. VP4 is interior and not visible in this

of VP1 are found at each fivefold axis (compare Fig. 2.7 with

view. This figure was kindly provided by Dr. Michael Rossmann.

Fig. 2.8). VP1, VP2, and VP3 are structurally related to one

another, as stated, all possessing the common β-sandwich

fold. There exists a depression around each fivefold axis of

rhinoviruses that has been termed a "canyon." This depres-

Atomic Structure of Polyomaviruses

sion is believed to be the site at which the virus interacts with

The structures of both mouse polyomavirus and of

the cellular receptor during entry, as illustrated in Fig. 2.9.

SV40 virus, two members of the family Polyomaviridae,

This interaction is thought to lead to conformational changes

have been solved to atomic resolution. Both viruses pos-

that open a channel at the fivefold axis, through which VP4

sess pseudo-T=7 icosahedral symmetry. Although T=7

is extruded, followed by the viral RNA.

T=3

Poliovirus

Cowpea Mosaic Virus

VP1

VP3

VP2

VP1

VP2

VP3

VP2

VP3

VP1

VP3

VP2

VP2

VP3

VP1

VP3

VP2

VP1

VP2

VP3

VP1

VP2

VP3

VP1

VP2

VP3

VP1

VP2

VP1

VP3

VP2 VP1 VP1 VP3

VP3 VP2

FIGURE 2.7 Arrangement of the coat protein subunits of comoviruses compared with those of simple T=3 viruses and

picornaviruses. In simple viruses, the asymmetric unit contains three copies of a single protein β sandwich, labeled A, B,

and C in order to distinguish them. In picornaviruses such as poliovirus the asymmetric unit is made up of three similar

but not identical proteins, all of which have the β-sandwich structure. In comoviruses such as cowpea mosaic virus, two

of the β-sandwich subunits are fused to give the L protein. Adapted from Granoff and Webster (1999), p. 287.

ICAM-1

VP1

"Canyon''

VP2

Drug-binding pocket

VP3 bcylinder

VP3

VP4

RNA

Five-fold Axis

FIGURE 2.9 Binding of the rhinovirus receptor, ICAM-1, to the "canyon" at a fivefold vertex of a virion of a major

group human rhinovirus. The colors of the three virion proteins are the same as those shown in the surface view in Fig.

2.8. The distal two domains of ICAM-1 are represented schematically (cross-hatched) as they were in Fig. 1.5. The

amino-terminal domains of the five VP3 molecules around the fivefold axis form a five-stranded β cylinder on the virion's

interior and are thought to stabilize the pentamer. Below the canyon is the hydrophobic pocket where certain antiviral

drugs (indicated schematically in black) are known to bind. Adapted from Kolatkar et al. (1999).

symmetry would require 420 subunits, these viruses con-

solve the structure of one or more members of three gen-

tain only 360 copies of a major structural protein known

era within the Reoviridae, namely Reovirus, Rotavirus, and

as VP1. These 360 copies are assembled as 72 pentamers.

Orbivirus, to about 25-Å resolution. Structures of a reovirus

Twelve of the 72 pentamers lie on the fivefold axes and

and of a rotavirus are shown in Fig. 2.5. The complete struc-

the remaining 60 fill the intervening surface in a closely

ture of virions has not been determined because of their large

packed array (Fig. 2.10). These latter pentamers are thus

size, but in a remarkable feat the atomic structure of the core

sixfold coordinated and the proteins in the shell are not all

of bluetongue virus (genus Orbivirus) has now been solved.

in quasi-equivalent positions, a surprising finding for our

This is the largest structure determined to atomic resolu-

understanding of the principles by which viruses can be

tion to date. Solution of the structure was possible because

constructed. The pentamers are stabilized by interactions

the virus particle had been solved to 25 Å by cryoelectron

of the β sheets between adjacent monomers in a pentamer

microscopy, and the structures of a number of virion proteins

(Fig. 2.10C). The pentamers are then tied together by

had been solved to atomic resolution by X-ray diffraction.

C-terminal arms of VP1 that invade monomers in an adja-

Fitting the atomic structure of the proteins into the 25-Å

cent pentamer (Figs. 2.10B and C). Because each pentamer

structure gave a preliminary reconstruction at high resolu-

that is sixfold coordinated has five C-terminal arms to

tion, which allowed the interpretation of the X-ray data to

interact with six neighboring pentamers, the interactions

atomic resolution.

between monomers in different pentamers are not all iden-

Core particles are formed following infection, when the

tical (Fig. 2.10B). Flexibility in the C-terminal arm allows

outer layer is proteolytically cleaved (described in more

it to form contacts in different ways.

detail in Chapter 5). The structure of the inner surface of

the bluetongue virus core is shown in Fig. 2.11A and of the

outer surface in Fig. 2.11B. The outer surface is formed by

Atomic Structure of Bluetongue Virus

780 copies of a single protein, called VP7, in a regular T=13

Members of the reovirus family are regular T=13 icosahe-

icosahedral lattice. The inner surface is surprising, however.

dral particles. They are composed of two or three concentric

It is formed by 120 copies of a single protein, called VP3.

protein shells. Cryoelectron microscopy has been used to

These 120 copies have been described as forming a T=2

a,,

Pentamer axis

b sheet from adjacent

VP1 in same pentamer

Red and blue arrows are b sheets

C-terminal domain from an

adjacent pentamer

FIGURE 2.10 Organization of the capsid of the polyomavirus SV40. (A) Arrangement of the strict pentamers (white)

and quasi pentamers (colored) on the T=7d icosahedral lattice. (B) Schematic showing the pattern of interchange of arms

in the virion. The central pentamer shares "arms" with six neighboring pentamers. (C) A single VP1 subunit, viewed

normal to the pentamer axis. The N-terminal domain is green, the C-terminal domain is yellow, and the β sandwich is

shown as arrows of blue and red. The central yellow C-terminal domain (outlined in black) comes from an adjacent

pentamer and the β sheet outlined in black comes from the neighboring VP1 within the same pentamer. From Figure 1

Stehle et al. (1996) and Fields et al. (1996), Color Plate 4.

Structure of Adenoviruses

lattice. Because T=2 is not a permitted triangulation number,

these 120 copies, strictly speaking, form a T=1 lattice in

Cryoelectron microscopy has also been applied to adeno-

which each unit of the lattice is composed of two copies of

viruses, which have a triangulation number of 25 or pseudo-

VP3. However, the interactions are not symmetrical, leading

25. Various interpretations of the structure of adenoviruses,

to the suggested terminology of T=2.

both schematic and as determined by microscopy or crystal-

It has been suggested that the inner core furnishes a template

lography, are shown in Fig. 2.12. Three copies of a protein

for the assembly of the T=13 outer surface. The reasoning is

called the hexon protein associate to form a structure called a

that a T=13 structure may have difficulty in forming, whereas

hexon (Fig. 2.12C). The hexon is the basic building block of

the T=2 (or T=1) structure could form readily. In this model,

adenoviruses. Five hexons, called peripentonal hexons, sur-

the threefold symmetry axis of the inner surface could serve to

round each of the 12 vertices of the icosahedron (which, as has

nucleate VP7 trimers and organize the T=13 structure.

been stated, have fivefold rotational symmetry). Between the

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