![Illustration of the Caspar-Klug model for viruses (or](https://upload.wikimedia.org/wikipedia/commons/c/c2/Illustration_of_the_Caspar-Klug_model_for_viruses_%28or_%22Goldberg_Polyhedra%22_or_%22Geodesic_domes%22_or_%22Fullerenes%22%29.gif)
A capsid is the protein shell of a
virus
A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea.
Since Dmitri Ivanovsky's 1 ...
, enclosing its
genetic material
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main cla ...
. It consists of several
oligomer
In chemistry and biochemistry, an oligomer () is a molecule that consists of a few repeating units which could be derived, actually or conceptually, from smaller molecules, monomers.Quote: ''Oligomer molecule: A molecule of intermediate relativ ...
ic (repeating) structural subunits made of
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
called
protomer
In structural biology, a protomer is the structural unit of an oligomeric protein. It is the smallest unit composed of at least two different protein chains that form a larger hetero-oligomer by association of two or more copies of this unit.
The ...
s. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called
capsomere
The capsomere is a subunit of the capsid, an outer covering of protein that protects the genetic material of a virus. Capsomeres self-assemble to form the capsid.
Subunits called protomers aggregate to form capsomeres. Various arrangements of ca ...
s. The proteins making up the capsid are called capsid proteins or viral coat proteins (VCP). The capsid and inner
genome
In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ge ...
is called the nucleocapsid.
Capsids are broadly classified according to their structure. The majority of the viruses have capsids with either
helical
Helical may refer to:
* Helix, the mathematical concept for the shape
* Helical engine, a proposed spacecraft propulsion drive
* Helical spring, a coilspring
* Helical plc, a British property company, once a maker of steel bar stock
* Helicoil
A t ...
or
icosahedral
In geometry, an icosahedron ( or ) is a polyhedron with 20 faces. The name comes and . The plural can be either "icosahedra" () or "icosahedrons".
There are infinitely many non- similar shapes of icosahedra, some of them being more symmetrica ...
structure. Some viruses, such as
bacteriophage
A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bacteri ...
s, have developed more complicated structures due to constraints of elasticity and electrostatics. The icosahedral shape, which has 20 equilateral triangular faces, approximates a
sphere
A sphere () is a Geometry, geometrical object that is a solid geometry, three-dimensional analogue to a two-dimensional circle. A sphere is the Locus (mathematics), set of points that are all at the same distance from a given point in three ...
, while the helical shape resembles the shape of a
spring
Spring(s) may refer to:
Common uses
* Spring (season), a season of the year
* Spring (device), a mechanical device that stores energy
* Spring (hydrology), a natural source of water
* Spring (mathematics), a geometric surface in the shape of a ...
, taking the space of a cylinder but not being a cylinder itself. The capsid faces may consist of one or more proteins. For example, the
foot-and-mouth disease
Foot-and-mouth disease (FMD) or hoof-and-mouth disease (HMD) is an infectious and sometimes fatal viral disease that affects cloven-hoofed animals, including domestic and wild bovids. The virus causes a high fever lasting two to six days, followe ...
virus capsid has faces consisting of three proteins named VP1–3.
Some viruses are ''enveloped'', meaning that the capsid is coated with a lipid membrane known as the ''
viral envelope
A viral envelope is the outermost layer of many types of viruses. It protects the genetic material in their life cycle when traveling between host cells. Not all viruses have envelopes.
Numerous human pathogenic viruses in circulation are encase ...
''. The envelope is acquired by the capsid from an intracellular membrane in the virus' host; examples include the inner nuclear membrane, the
Golgi membrane, and the cell's outer
membrane
A membrane is a selective barrier; it allows some things to pass through but stops others. Such things may be molecules, ions, or other small particles. Membranes can be generally classified into synthetic membranes and biological membranes. B ...
.
Once the virus has infected a cell and begins replicating itself, new capsid subunits are synthesized using the
protein biosynthesis
Protein biosynthesis (or protein synthesis) is a core biological process, occurring inside cells, balancing the loss of cellular proteins (via degradation or export) through the production of new proteins. Proteins perform a number of critical ...
mechanism of the cell. In some viruses, including those with helical capsids and especially those with RNA genomes, the capsid proteins co-assemble with their genomes. In other viruses, especially more complex viruses with double-stranded DNA genomes, the capsid proteins assemble into empty precursor procapsids that include a specialized portal structure at one vertex. Through this portal, viral
DNA is translocated into the capsid.
Structural analyses of major capsid protein (MCP) architectures have been used to categorise viruses into lineages. For example, the bacteriophage PRD1, the algal virus ''
Paramecium bursaria Chlorella virus-1'' (PBCV-1),
mimivirus
''Mimivirus'' is a genus of giant viruses, in the family ''Mimiviridae''. Amoeba serve as their natural hosts. This genus contains a single identified species named ''Acanthamoeba polyphaga mimivirus'' (APMV). It also refers to a group of phylo ...
and the mammalian
adenovirus
Adenoviruses (members of the family ''Adenoviridae'') are medium-sized (90–100 nm), nonenveloped (without an outer lipid bilayer) viruses with an icosahedral nucleocapsid containing a double-stranded DNA genome. Their name derives from the ...
have been placed in the same lineage, whereas tailed, double-stranded DNA bacteriophages (''
Caudovirales
''Caudovirales'' is an order of viruses known as the tailed bacteriophages (''cauda'' is Latin for "tail"). Under the Baltimore classification scheme, the ''Caudovirales'' are group I viruses as they have double stranded DNA (dsDNA) genomes, ...
'') and herpesvirus belong to a second lineage.
Specific shapes
Icosahedral
![Adenovirus 3D schematic](https://upload.wikimedia.org/wikipedia/commons/6/6a/Adenovirus_3D_schematic.png)
The icosahedral structure is extremely common among viruses. The
icosahedron
In geometry, an icosahedron ( or ) is a polyhedron with 20 faces. The name comes and . The plural can be either "icosahedra" () or "icosahedrons".
There are infinitely many non- similar shapes of icosahedra, some of them being more symmetrica ...
consists of 20 triangular faces delimited by 12 fivefold vertexes and consists of 60 asymmetric units. Thus, an icosahedral virus is made of 60N protein subunits. The number and arrangement of
capsomere
The capsomere is a subunit of the capsid, an outer covering of protein that protects the genetic material of a virus. Capsomeres self-assemble to form the capsid.
Subunits called protomers aggregate to form capsomeres. Various arrangements of ca ...
s in an icosahedral capsid can be classified using the "quasi-equivalence principle" proposed by
Donald Caspar
Donald L. D. Caspar (January 8, 1927 - November 27, 2021) was an American structural biologist (the very term he coined) known for his works on the structures of biological molecules, particularly of the tobacco mosaic virus. He was an emeritus p ...
and
Aaron Klug
Sir Aaron Klug (11 August 1926 – 20 November 2018) was a British biophysicist and chemist. He was a winner of the 1982 Nobel Prize in Chemistry for his development of crystallographic electron microscopy and his structural elucidation of bio ...
.
Like the
Goldberg polyhedra
In mathematics, and more specifically in polyhedral combinatorics, a Goldberg polyhedron is a convex polyhedron made from hexagons and pentagons. They were first described in 1937 by Michael Goldberg (mathematician), Michael Goldberg (1902–1990 ...
, an icosahedral structure can be regarded as being constructed from pentamers and hexamers. The structures can be indexed by two integers ''h'' and ''k'', with
and
; the structure can be thought of as taking ''h'' steps from the edge of a pentamer, turning 60 degrees counterclockwise, then taking ''k'' steps to get to the next pentamer. The triangulation number ''T'' for the capsid is defined as:
:
In this scheme, icosahedral capsids contain 12 pentamers plus 10(''T'' − 1) hexamers.
The ''T''-number is representative of the size and complexity of the capsids. Geometric examples for many values of ''h'', ''k'', and ''T'' can be found at
List of geodesic polyhedra and Goldberg polyhedra
This is a list of selected geodesic polyhedron, geodesic polyhedra and Goldberg polyhedron, Goldberg polyhedra, two infinite classes of polyhedron, polyhedra. Geodesic polyhedra and Goldberg polyhedra are polyhedral dual, duals of each other. The g ...
.
Many exceptions to this rule exist: For example, the
polyomavirus
''Polyomaviridae'' is a family of viruses whose natural hosts are primarily mammals and birds. As of 2020, there are six recognized genera and 117 species, five of which are unassigned to a genus. 14 species are known to infect humans, while othe ...
es and
papillomaviruses
''Papillomaviridae'' is a family of non- enveloped DNA viruses whose members are known as papillomaviruses. Several hundred species of papillomaviruses, traditionally referred to as "types", have been identified infecting all carefully inspected ...
have pentamers instead of hexamers in hexavalent positions on a quasi T = 7 lattice. Members of the double-stranded RNA virus lineage, including
reovirus
''Reoviridae'' is a family of double-stranded RNA viruses. Member viruses have a wide host range, including vertebrates, invertebrates, plants, protists and fungi. They lack lipid envelopes and package their segmented genome within multi-layered ...
,
rotavirus
''Rotavirus'' is a genus of double-stranded RNA viruses in the family ''Reoviridae''. Rotaviruses are the most common cause of diarrhoeal disease among infants and young children. Nearly every child in the world is infected with a rotavirus a ...
and bacteriophage φ6 have capsids built of 120 copies of capsid protein, corresponding to a T = 2 capsid, or arguably a T = 1 capsid with a dimer in the asymmetric unit. Similarly, many small viruses have a pseudo T = 3 (or P = 3) capsid, which is organized according to a T = 3 lattice, but with distinct polypeptides occupying the three quasi-equivalent positions
T-numbers can be represented in different ways, for example ''T'' = 1 can only be represented as an
icosahedron
In geometry, an icosahedron ( or ) is a polyhedron with 20 faces. The name comes and . The plural can be either "icosahedra" () or "icosahedrons".
There are infinitely many non- similar shapes of icosahedra, some of them being more symmetrica ...
or a
dodecahedron
In geometry, a dodecahedron (Greek , from ''dōdeka'' "twelve" + ''hédra'' "base", "seat" or "face") or duodecahedron is any polyhedron with twelve flat faces. The most familiar dodecahedron is the regular dodecahedron with regular pentagon ...
and, depending on the type of quasi-symmetry, ''T'' = 3 can be presented as a
truncated dodecahedron
In geometry, the truncated dodecahedron is an Archimedean solid. It has 12 regular decagonal faces, 20 regular triangular faces, 60 vertices and 90 edges.
Geometric relations
This polyhedron can be formed from a regular dodecahedron by truncat ...
, an
icosidodecahedron
In geometry, an icosidodecahedron is a polyhedron with twenty (''icosi'') triangular faces and twelve (''dodeca'') pentagonal faces. An icosidodecahedron has 30 identical vertices, with two triangles and two pentagons meeting at each, and 60 id ...
, or a
truncated icosahedron
In geometry, the truncated icosahedron is an Archimedean solid, one of 13 convex isogonal nonprismatic solids whose 32 faces are two or more types of regular polygons. It is the only one of these shapes that does not contain triangles or squares. ...
and their respective duals a
triakis icosahedron
In geometry, the triakis icosahedron (or kisicosahedronConway, Symmetries of things, p.284) is an Archimedean dual solid, or a Catalan solid. Its dual is the truncated dodecahedron.
Cartesian coordinates
Let \phi be the golden ratio. The 12 po ...
, a
rhombic triacontahedron
In geometry, the rhombic triacontahedron, sometimes simply called the triacontahedron as it is the most common thirty-faced polyhedron, is a convex polyhedron with 30 rhombic faces. It has 60 edges and 32 vertices of two types. It is a Cata ...
, or a
pentakis dodecahedron
In geometry, a pentakis dodecahedron or kisdodecahedron is the polyhedron created by attaching a pentagonal pyramid to each face of a regular dodecahedron; that is, it is the Kleetope of the dodecahedron. It is a Catalan solid, meaning that i ...
.
Prolate
An elongated icosahedron is a common shape for the heads of bacteriophages. Such a structure is composed of a cylinder with a cap at either end. The cylinder is composed of 10 elongated triangular faces. The Q number (or T
mid), which can be any positive integer, specifies the number of triangles, composed of asymmetric subunits, that make up the 10 triangles of the cylinder. The caps are classified by the T (or T
end) number.
The bacterium ''E. coli'' is the host for
bacteriophage T4
Escherichia virus T4 is a species of bacteriophages that infect ''Escherichia coli'' bacteria. It is a double-stranded DNA virus in the subfamily '' Tevenvirinae'' from the family Myoviridae. T4 is capable of undergoing only a lytic lifecycle ...
that has a prolate head structure. The bacteriophage encoded gp31 protein appears to be functionally homologous to ''E. coli'' chaperone protein GroES and able to substitute for it in the assembly of bacteriophage T4 virions during infection.
[Marusich EI, Kurochkina LP, Mesyanzhinov VV. Chaperones in bacteriophage T4 assembly. Biochemistry (Mosc). 1998;63(4):399-406] Like GroES, gp31 forms a stable complex with
GroEL
GroEL is a protein which belongs to the chaperonin family of molecular chaperones, and is found in many bacteria. It is required for the proper folding of many proteins. To function properly, GroEL requires the lid-like cochaperonin protein comp ...
chaperonin
HSP60, also known as chaperonins (Cpn), is a family of heat shock proteins originally sorted by their 60kDa molecular mass. They prevent misfolding of proteins during stressful situations such as high heat, by assisting protein folding. HSP60 bel ...
that is absolutely necessary for the folding and assembly ''in vivo'' of the bacteriophage T4 major capsid protein gp23.
[
]
Helical
Many rod-shaped and filamentous plant viruses have capsids with helical symmetry
In geometry, an object has symmetry if there is an operation or transformation (such as translation, scaling, rotation or reflection) that maps the figure/object onto itself (i.e., the object has an invariance under the transform). Thus, a symme ...
. The helical structure can be described as a set of ''n'' 1-D molecular helices related by an ''n''-fold axial symmetry. The helical transformation are classified into two categories: one-dimensional and two-dimensional helical systems. Creating an entire helical structure relies on a set of translational and rotational matrices which are coded in the protein data bank. Helical symmetry is given by the formula ''P'' = ''μ'' x ''ρ'', where ''μ'' is the number of structural units per turn of the helix, ''ρ'' is the axial rise per unit and ''P'' is the pitch of the helix. The structure is said to be open due to the characteristic that any volume can be enclosed by varying the length of the helix. The most understood helical virus is the tobacco mosaic virus. The virus is a single molecule of (+) strand RNA. Each coat protein on the interior of the helix bind three nucleotides of the RNA genome. Influenza A viruses differ by comprising multiple ribonucleoproteins, the viral NP protein organizes the RNA into a helical structure. The size is also different; the tobacco mosaic virus has a 16.33 protein subunits per helical turn, while the influenza A virus has a 28 amino acid tail loop.
Functions
The functions of the capsid are to:
* protect the genome,
* deliver the genome, and
* interact with the host.
The virus must assemble a stable, protective protein shell to protect the genome from lethal chemical and physical agents. These include extremes of pH or temperature and proteolytic and nucleolytic enzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...
s. For non-enveloped viruses, the capsid itself may be involved in interaction with receptors on the host cell, leading to penetration of the host cell membrane and internalization of the capsid. Delivery of the genome occurs by subsequent uncoating or disassembly of the capsid and release of the genome into the cytoplasm, or by ejection of the genome through a specialized portal structure directly into the host cell nucleus.
Origin and evolution
It has been suggested that many viral capsid proteins have evolved on multiple occasions from functionally diverse cellular proteins. The recruitment of cellular proteins appears to have occurred at different stages of evolution so that some cellular proteins were captured and refunctionalized prior to the divergence of cellular organisms into the three contemporary domains of life, whereas others were hijacked relatively recently. As a result, some capsid proteins are widespread in viruses infecting distantly related organisms (e.g., capsid proteins with the jelly-roll fold
The jelly roll or Swiss roll fold is a protein fold or supersecondary structure composed of eight beta strands arranged in two four-stranded sheets. The name of the structure was introduced by Jane S. Richardson in 1981, reflecting its resemblanc ...
), whereas others are restricted to a particular group of viruses (e.g., capsid proteins of alphaviruses).
A computational model (2015) has shown that capsids may have originated before viruses and that they served as a means of horizontal transfer between replicator communities since these communities could not survive if the number of gene parasites increased, with certain genes being responsible for the formation of these structures and those that favored the survival of self-replicating communities. The displacement of these ancestral genes between cellular organisms could favor the appearance of new viruses during evolution.
See also
* Geodesic polyhedron
A geodesic polyhedron is a convex polyhedron made from triangles. They usually have icosahedral symmetry, such that they have 6 triangles at a vertex, except 12 vertices which have 5 triangles. They are the dual of corresponding Goldberg polyhed ...
* Goldberg–Coxeter construction
The Goldberg–Coxeter construction or Goldberg–Coxeter operation (GC construction or GC operation) is a graph operation defined on regular polyhedral graphs with degree 3 or 4. It also applies to the dual graph of these graphs, i.e. graphs wit ...
* Fullerene#Other buckyballs
References
Further reading
*
*
*
External links
IRAM-Virus Capsid Database and Analysis Resource
{{Authority control
Virology
Protein complexes