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Capsid
Capsid
Capsid
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Schematic of a cytomegalovirus
Illustration of geometric model changing between two possible capsids. A similar change of size has been observed as the result of a single amino-acid mutation[1]

A capsid is the protein shell of a virus, enclosing its genetic material. It consists of several oligomeric (repeating) structural subunits made of protein called protomers. The observable 3-dimensional morphological subunits, which may or may not correspond to individual proteins, are called capsomeres. The proteins making up the capsid are called capsid proteins or viral coat proteins (VCP). The virus genomic component inside the capsid, along with occasionally present virus core protein, is called the virus core. The capsid and core together are referred to as a nucleocapsid (cf. also virion).

Capsids are broadly classified according to their structure. The majority of the viruses have capsids with either helical or icosahedral[2][3] structure. Some viruses, such as bacteriophages, have developed more complicated structures due to constraints of elasticity and electrostatics.[4] The icosahedral shape, which has 20 equilateral triangular faces, approximates a sphere, while the helical shape resembles the shape of a spring, taking the space of a cylinder but not being a cylinder itself.[5] The capsid faces may consist of one or more proteins. For example, the foot-and-mouth disease virus capsid has faces consisting of three proteins named VP1–3.[6]

Some viruses are enveloped, meaning that the capsid is coated with a lipid membrane known as the viral envelope. 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.[7]

Once the virus has infected a cell and begins replicating itself, new capsid subunits are synthesized using the protein biosynthesis 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.[8]

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 and the mammalian adenovirus have been placed in the same lineage, whereas tailed, double-stranded DNA bacteriophages (Caudovirales) and herpesvirus belong to a second lineage.[9][10][11][12]

Specific shapes

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Icosahedral

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Icosahedral capsid of an adenovirus
Virus capsid T-numbers

The icosahedral structure is extremely common among viruses. The icosahedron 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 capsomeres in an icosahedral capsid can be classified using the "quasi-equivalence principle" proposed by Donald Caspar and Aaron Klug.[13] Like the Goldberg polyhedra, 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.[14][15] The T-number is representative of the size and complexity of the capsids.[16] Geometric examples for many values of h, k, and T can be found at List of geodesic polyhedra and Goldberg polyhedra.

Many exceptions to this rule exist: For example, the polyomaviruses and papillomaviruses have pentamers instead of hexamers in hexavalent positions on a quasi T = 7 lattice. Members of the double-stranded RNA virus lineage, including reovirus, rotavirus 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 [17]

Prolate

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The prolate structure of a typical head on a bacteriophage

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 Tmid), which can be any positive integer,[18] 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 Tend) number.[19]

The bacterium E. coli is the host for bacteriophage T4 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.[20] Like GroES, gp31 forms a stable complex with GroEL chaperonin that is absolutely necessary for the folding and assembly in vivo of the bacteriophage T4 major capsid protein gp23.[20]

Helical

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3D model of a helical capsid structure of a virus

Many rod-shaped and filamentous plant viruses have capsids with helical symmetry.[21] The helical structure can be described as a set of n 1-D molecular helices related by an n-fold axial symmetry.[22] The helical transformation are classified into two categories: one-dimensional and two-dimensional helical systems.[22] Creating an entire helical structure relies on a set of translational and rotational matrices which are coded in the protein data bank.[22] 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.[23] The most understood helical virus is the tobacco mosaic virus.[21] The virus is a single molecule of (+) strand RNA. Each coat protein on the interior of the helix binds three nucleotides of the RNA genome, with the overall polymer having a μ value of 16.33 protein subunits per helical turn.[21] Influenza A viruses differ by comprising multiple ribonucleoproteins which organize the segmented RNA into double helical structures.[24]

Functions

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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 enzymes. 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

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It has been suggested that many viral capsid proteins have evolved on multiple occasions from functionally diverse cellular proteins.[25] 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), whereas others are restricted to a particular group of viruses (e.g., capsid proteins of alphaviruses).[25][26]

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.[27] The displacement of these ancestral genes between cellular organisms could favor the appearance of new viruses during evolution.[26]

See also

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References

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Further reading

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Revisions and contributorsEdit on WikipediaRead on Wikipedia

Capsid

View on Grokipedia
from Grokipedia
A capsid is the protein shell that encloses and protects the genetic material (genome) of a virus, serving as a nanoscale container that safeguards the nucleic acid from environmental damage during transmission between host cells. Composed primarily of multiple copies of one or more viral proteins known as protomers, which self-assemble into larger structural units called capsomeres, the capsid exhibits precise geometric symmetry to achieve stability and efficiency in packaging the genome. Viral capsids display a variety of shapes, with the most common being icosahedral (a polyhedral structure with 20 triangular faces, providing maximal volume with minimal surface area) and helical (a cylindrical or rod-like form where proteins coil around the elongated nucleic acid), while some viruses feature more complex or irregular architectures. These shapes are determined by the virus family and contribute to the overall virion morphology, influencing infectivity, stability, and host recognition. In non-enveloped viruses, the capsid forms the complete outer layer, whereas in enveloped viruses, it lies beneath a lipid membrane derived from the host cell. Beyond protection, capsids play critical roles in the viral lifecycle, including facilitating genome delivery into new host cells through disassembly (uncoating) upon entry and, in some cases, mediating attachment to host receptors via surface proteins. The assembly of capsids occurs rapidly and spontaneously in infected cells, driven by protein-protein interactions and often coupled with genome packaging, which requires overcoming electrostatic repulsions between the negatively charged nucleic acid and the positively charged inner capsid surface. Due to their structural uniformity and mechanical resilience—exhibiting properties like elasticity and rigidity—capsids have become models for studying biomolecular self-assembly and inspire applications in nanotechnology, such as drug delivery vehicles.

Definition and Composition

What is a Capsid

A capsid is the protein shell that encloses and protects the genetic material of a virus, which can be either DNA or RNA. This structure serves as the primary protective barrier for the viral genome against environmental damage and host defenses, and it is essential for the virus's ability to infect host cells. While many viruses are non-enveloped and consist solely of the capsid surrounding the nucleic acid, others are enveloped, where the capsid forms an internal core surrounded by a lipid membrane derived from the host cell. The capsid is distinct from the nucleocapsid, which refers to the complex of the capsid and its enclosed nucleic acid, and from the virion, which is the complete infectious virus particle that may include an outer envelope in addition to the nucleocapsid. In non-enveloped viruses, the virion is equivalent to the nucleocapsid, whereas in enveloped viruses, the capsid remains an internal component of the larger virion structure. The term "capsid" was coined in the mid-20th century, specifically with its first known use in 1959, derived from the Latin word capsa, meaning "box," reflecting its role as a container for the viral genome. Viral capsids were first visualized in the late 1930s and 1940s using the newly developed electron microscope, which allowed researchers to observe the particulate nature of viruses beyond the resolution of light microscopy. Capsids vary in size, typically ranging from 20 to 300 nanometers in diameter, depending on the virus type and its architectural complexity. For example, the poliovirus features a simple naked icosahedral capsid approximately 30 nanometers in diameter, consisting of 60 copies each of four proteins that form a symmetric shell around its RNA genome. In contrast, the human immunodeficiency virus (HIV) has a more complex conical capsid core about 50-60 nanometers wide at its base, which houses the RNA genome and is surrounded by an envelope in the mature virion.

Protein Subunits and Capsomeres

Capsid protein subunits, also known as protomers, are the fundamental building blocks of viral capsids, consisting of individual polypeptide chains or small oligomers that self-assemble to form the protective shell around the viral genome. These protomers are typically encoded by one or a few viral genes and exhibit high sequence variability across virus families, yet they share common structural features that enable stable assembly. In many cases, protomers aggregate into larger oligomeric clusters called capsomeres, which appear as distinct morphological units under electron microscopy and represent the visible repeating subunits of the capsid surface. A prevalent structural motif among capsid protomers is the jelly-roll β-barrel fold, an eight-stranded antiparallel β-sheet structure that forms a compact barrel-like domain, providing rigidity and facilitating inter-subunit interactions. This fold is particularly characteristic of non-enveloped viruses in the Picornavirales order, where the major capsid proteins VP1, VP2, and VP3 each adopt this conformation, with flexible loops and extensions allowing adaptation to different viral architectures. Chemically, capsid protomers are composed almost entirely of proteins, often as unglycosylated polypeptides but sometimes bearing N- or O-linked glycans that influence stability or host interactions; their molecular weights generally range from 10 to 100 kDa per subunit, enabling efficient packaging within the nanoscale confines of the virion. Non-enveloped capsids, by definition, exclude lipids, distinguishing them from the lipid-bilayer envelopes of other viruses. The number of protomers in a capsid varies with viral size and complexity, with the simplest icosahedral structures incorporating 60 identical or quasi-identical subunits arranged in a symmetric shell. Larger capsids employ multiples of this base number, such as 180 or 540 subunits, to expand surface area while maintaining structural integrity. A representative example is the foot-and-mouth disease virus (FMDV), an aphtovirus in the Picornaviridae family, whose capsid comprises 60 copies each of four protomers: VP1, VP2, VP3, and VP4. In FMDV, VP1 protrudes from the surface and mediates receptor binding via its exposed GH loop, VP2 and VP3 form the bulk of the capsomere interfaces with roles in antigenicity and stability, and VP4 resides internally, associating closely with the RNA genome. These subunits collectively shield the viral genome from nucleases and environmental stressors, ensuring infectivity.

Symmetry and Architecture

Principles of Viral Symmetry

Viral capsids adopt symmetric architectures to organize multiple copies of protein subunits into stable, efficient enclosures for the viral genome. The primary types of symmetry observed are icosahedral and helical, with some viruses exhibiting more complex or irregular symmetries. Icosahedral symmetry, characterized by five-fold, three-fold, and two-fold rotational axes, predominates in spherical viruses, enabling a closed shell that evenly distributes structural strain across identical subunits. Helical symmetry, in contrast, generates elongated, cylindrical structures ideal for viruses with linear genomes, where subunits align in a repeating spiral pattern around the nucleic acid. These symmetric principles ensure geometric consistency while accommodating the functional needs of diverse viral families. The biological rationale for symmetry in capsid formation lies in its ability to maximize efficient packing of protein subunits around the irregular shape of the nucleic acid, thereby minimizing free energy during self-assembly and enhancing structural stability. Symmetric arrangements allow a small number of subunit types to form large, closed structures without gaps or overlaps, optimizing resource use in the constrained genetic economy of viruses. This efficiency is particularly crucial for non-enveloped viruses, where the capsid must withstand environmental stresses independently. By enforcing equivalent bonding interactions among subunits, symmetry reduces conformational variability and promotes rapid, error-free assembly in the host cell. The foundational framework for understanding these symmetries, particularly icosahedral ones, is the Caspar-Klug theory proposed in 1962, which predicts allowable symmetric structures based on quasi-equivalent interactions between identical protein subunits arranged on an icosahedral lattice. This theory posits that subunits adopt slightly distorted conformations to maintain similar bonding domains, enabling the formation of polyhedral shells with 12 pentavalent vertices and variable hexagonal faces. For icosahedral capsids, asymmetry elements such as pentons—clusters of five subunits at the 12 five-fold rotational vertices—and hexons—clusters of six subunits at the six-fold axes—define the core structural motifs that enforce overall symmetry. The simplest application is seen in T=1 capsids, where 60 subunits form a basic icosahedron without hexagonal elaboration. Recent advancements in cryo-electron microscopy (cryo-EM) have revolutionized the visualization of these symmetric principles, achieving near-atomic resolution of capsid arrangements in non-enveloped viruses and revealing subtle deviations or enforcements of symmetry at the molecular level. These high-resolution structures have clarified how symmetric lattices accommodate dynamic processes like genome packaging, with techniques such as single-particle analysis and subtomogram averaging enabling the mapping of subunit interfaces in unprecedented detail. Such insights confirm the predictive power of classical theories while highlighting symmetry's role in functional adaptability.

Quasi-equivalence and T-numbers

The quasi-equivalence principle, proposed by Donald Caspar and Aaron Klug in 1962, addresses the challenge of assembling icosahedral viral capsids using identical protein subunits in non-identical environments. This principle posits that subunits adopt slightly different conformations to occupy geometrically equivalent positions on the capsid surface, thereby enabling the closure of a symmetric shell while minimizing strain from identical bonding geometries. By allowing local adjustments in subunit bonds and shapes, quasi-equivalence facilitates efficient use of a single protein type to form large, stable structures, as observed in many small icosahedral viruses. Central to this framework is the triangulation number TT, which quantifies the size and subunit arrangement in icosahedral lattices. Defined as T=h2+hk+k2T = h^2 + hk + k^2, where hh and kk are nonnegative integers representing steps along the icosahedral lattice vectors, TT determines the total number of protein subunits as 60T60T. For instance, the simplest T=1T=1 structure (where h=1h=1, k=0k=0) consists of 60 subunits arranged in 12 pentamers, while T=3T=3 (e.g., h=1h=1, k=1k=1) expands to 180 subunits, incorporating 12 pentamers and 20 hexamers to increase the capsid radius. This parameterization allows for a systematic classification of capsid architectures, with larger TT values corresponding to bigger viruses that accommodate more genetic material. The internal volume of an icosahedral capsid can be approximated as that of a sphere, V≈43πr3V \approx \frac{4}{3} \pi r^3, where the radius rr scales with T\sqrt{T}
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