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30-499: The virions in this family have a capsid with icosahedral geometry and a viral envelope that protects the genetic material . The diameter is 83 to 87 nanometers. The genome is circular dsDNA with a length of 20,222 base pairs. The genome contains 45 open reading frames (ORFs), which are closely arranged and occupy 89.1% of the genome. ORFs are generally short, with an average length of 103 codons . Virions have 10 proteins ranging from 20 to 32 kDa. Of these proteins, 8 code for

60-399: A lipid bilayer and surface proteins similar to the cell membranes (that are usually used for the envelope construction when the virus is exiting the cell). This structure helps with attachment to the cell and also assists evading the immune system of the host organism while the virion is searching for the cell to infect. Triangulation number A capsid is the protein shell of

90-432: A sphere , while the helical shape resembles the shape of a spring , 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 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 . The envelope

120-419: A truncated icosahedron and their respective duals a triakis icosahedron , a rhombic triacontahedron , or a pentakis dodecahedron . 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

150-410: 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 capsid and inner genome

180-450: A 16.33 protein subunits per helical turn, while the influenza A virus has a 28 amino acid tail loop. The functions of the capsid are to: 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

210-445: 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 or a dodecahedron and, depending on the type of quasi-symmetry, T  = 3 can be presented as a truncated dodecahedron , an icosidodecahedron , or

240-403: 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

270-477: 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 . 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,

300-448: Is an inert virus particle capable of invading a cell . Upon entering the cell, the virion disassembles, and the genetic material of the virus takes control of the cell infrastructure, thus enabling the virus to replicate . The genetic material ( core , either DNA or RNA ) inside virion is usually enclosed in a protection shell, so called capsid . While the terms " virus " and "virion" are occasionally confused, recently "virion"

330-404: Is called the nucleocapsid . Capsids are broadly classified according to their structure. The majority of the viruses have capsids with either helical or icosahedral structure. Some viruses, such as bacteriophages , have developed more complicated structures due to constraints of elasticity and electrostatics. The icosahedral shape, which has 20 equilateral triangular faces, approximates

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360-586: 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 . 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 h ≥ 1 {\displaystyle h\geq 1} and k ≥ 0 {\displaystyle k\geq 0} ;

390-479: Is used solely to describe the virus structure outside of cells, while the terms "virus/viral" are broader and also include biological properties such as the infectivity of a virion. A virion consists of one or more nucleic acid genome molecules (single-stranded or double-stranded RNA or DNA ) and coatings (a capsid and possibly a viral envelope ). The virion may contain other proteins (for example with enzymatic activities) and/or nucleoproteins . In

420-523: The Coronaviridae , the Tectiviridae and others. These are used to establish contact with the host cell. In viruses of the genus Chlorovirus , the virions have a single spike that serves as an injection device; extendable injection apparatus are found in virions of the family Tectiviridae . In many virus species the virion also has an outer membrane, the viral envelope . The envelope includes

450-514: The faces of a polyhedron . Each face in turn is formed by a repetition of simpler sub-units, with the amount of repetitions called a triangulation number (T). Similar capsid structure can be used by many different types of viruses. In many viruses, the virions have icosahedral symmetry , which can be ideally isometric or elongated. Many virions also have other shapes: From observations using microscopy , there are indications of many more distinct shapes. In some groups of viruses - such as

480-528: The Citrus Bark Crack Viroid ). If the genome consists of several segments, these are usually packaged together in a capsid (like in the influenza viruses ), in some viruses the segments can also be individually packaged in their own capsids (for example, in Nanoviridae ). Since the genome of viruses is relatively simple, the capsid architecture relies on repetition of simple structures, similar to

510-515: The Enterobacteria phage lambda , in addition there may be a tail spike protein (TSP) or tail fiber protein (TFP). Even in viruses with helical morphology (such as the Rudiviridae and Ahmunviridae ), the terminal fiber proteins responsible for the receptor binding are called tail fiber proteins ( tail fiber proteins ). So-called spikes (peplomers) can protrude from the capsid, as in

540-417: 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

570-613: The assembly of bacteriophage T4 virions during infection. 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. Many rod-shaped and filamentous plant viruses have capsids with helical symmetry . 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

600-501: 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. 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

630-421: The capsid and two for the viral envelope, including one that is a vertical single jelly roll (SJR) capsid protein . Entry into the host cell is by penetration. Viral replication occurs by chronic infection without a lytic cycle . The Portogloboviridae viruses together with Halopanivirales have evolutionary importance in the evolution of the other Varidnaviria viruses since they appear to be relics of how

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660-455: 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,

690-537: The class Caudoviricetes ("tail viruses") and the genus Tupanvirus - the capsid carries an appendage called the "tail". The tail of the Caudoviricetes is usually divided into The latter are used to establish contact with the host cell. The tail of these viruses serves as an injection device to introduce their own genome into the host cell. The Caudoviricetes tail material is also differentiated into major and minor tail proteins (MTP and mTP), for example, in

720-500: 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). A computational model (2015) has shown that capsids may have originated before viruses and that they served as

750-462: The first viruses of this realm were. Portogloboviridae together with Halopanivirales may have infected the last universal common ancestor (LUCA) and originated before that organism. It has been proposed that it may be related to the origin of Varidnaviria in the following way. Portogloboviridae Helvetiavirae Bamfordvirae The family has one genus which has two species: Virion A virion (plural viria or virions ),

780-639: 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. 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

810-468: 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

840-450: 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 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

870-578: 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 . Many exceptions to this rule exist: For example,

900-686: The vast majority of viruses, the DNA and RNA components are packed into a protein shell, the capsid . The capsid proteins are often differentiated into major and minor capsid proteins (MCP and mCP). In exceptional cases, there are also viruses without a capsid (i.e., true virions), such as the RNA viruses of the Narnaviridae and the viroids of the Pospiviroidae (with the Citrus Exocortis Viroid and

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