Virus Structure: Labeled Diagrams and 3D Models

A virus particle, called a virion, is made of a genome (DNA or RNA, never both) enclosed in a protein coat called the capsid. The capsid is built from many repeating protein subunits called capsomeres. The genome and capsid together are the nucleocapsid. Many viruses also have a lipid envelope around the nucleocapsid, studded with glycoprotein spikes (peplomers), and some have a matrix protein layer under the envelope and enzymes packed inside.

That is the whole list. A virion has no cytoplasm, no ribosomes, no mitochondria and no metabolism. Its job is to protect the genome outside a cell, find the right host cell, and deliver the genome inside. Everything else happens inside the host cell, using the host's machinery.

Two simple rules help when you label a diagram. First, if a part is made of lipid, it came from the host cell; if it is protein or nucleic acid, it is encoded by the virus. Second, only the envelope is optional for the virus to count as complete: some viruses are "naked" (non-enveloped), but no virus is without a capsid and a genome.

A labeled diagram of an enveloped virus shows, from outside in: the glycoprotein spikes, the lipid envelope, the matrix protein layer, the capsid made of capsomeres, and the nucleic acid genome inside, often with a viral enzyme bound to it. This is the generic textbook picture; real viruses vary the theme, as the 3D models above show.

The influenza model in the viewer is the real-life version of this diagram. Its envelope carries two kinds of spike, hemagglutinin (HA, blue) and neuraminidase (NA, red), plus a few M2 ion channels. The matrix protein M1 lines the envelope. Instead of one icosahedral capsid, influenza has eight separate helical nucleocapsids (RNPs), each an RNA segment wrapped around nucleoprotein, with a polymerase at one end. Use the tabs to compare it with HIV, SARS-CoV-2, a naked adenovirus and the helical tobacco mosaic virus.

This is the text version of the five 3D models: every labeled structure, grouped by virus and by layer, with what it does. Use it to revise or to check a labeled virus structure diagram.

Virus capsids come in three basic architectures: helical (a rod or filament), icosahedral (a closed, roughly spherical shell with 20 triangular faces and 12 corners), and complex (anything that is not simply one or the other). OpenStax uses tobacco mosaic virus as the helical example and bacteriophage T4 and poxviruses as complex examples.

Helical capsids

In a helical capsid, identical protein subunits stack in a spiral around the genome, like steps of a spiral staircase, and the nucleic acid runs in a groove between the turns. The length of the rod is set by the length of the genome. Tobacco mosaic virus is the classic case: a rigid rod about 300 nm long and 18 nm wide, built from about 2,130 coat-protein subunits, 16⅓ per turn, each binding three nucleotides of RNA. Many enveloped RNA viruses (influenza, measles, rabies, Ebola) also have helical nucleocapsids, but these are flexible and coiled up inside the envelope, so the virion itself is not rod-shaped.

Icosahedral capsids and the triangulation number

An icosahedron is the most efficient way to build a closed shell from many copies of one small protein. The simplest one has 60 identical subunits, three per face. Bigger capsids use more subunits in slightly different (quasi-equivalent) positions. The triangulation number, T, counts how many of these positions there are per face: T = h² + hk + k², where h and k are whole numbers that describe how many steps you take on the surface lattice from one corner (pentamer) to the next. Allowed values are 1, 3, 4, 7, 9, 12, 13 and so on. A capsid with triangulation number T is made of 60T subunits, arranged as 12 pentamers (always 12, at the corners) plus 10(T − 1) hexamers.

"Pseudo" means that the subunits are not all the same protein but the lattice has the same geometry. In adenovirus, each hexon is a trimer of one large protein with a six-sided base, so it fills a hexamer position without being six copies of one subunit.

Complex viruses

Complex viruses do not fit either plan. Bacteriophage T4 has an icosahedral (elongated) head attached to a helical tail with a baseplate and tail fibres; see our bacteriophage diagram for its structure. Poxviruses, including vaccinia and mpox, are large brick-shaped particles, about 250 × 200 nm, with surface tubules and several membranes, and no simple capsid symmetry.

An enveloped virus has a lipid membrane around its nucleocapsid; a non-enveloped or naked virus does not, so its capsid is the outermost layer. The envelope is acquired when the virus buds through a host-cell membrane, usually the plasma membrane (influenza, HIV) or an internal membrane, such as the ER–Golgi compartment used by coronaviruses.

Envelope and capsid shape are independent features. Influenza and measles are enveloped viruses with helical nucleocapsids; herpesviruses and hepatitis B are enveloped viruses with icosahedral capsids; adenovirus and poliovirus are naked icosahedral viruses; tobacco mosaic virus is a naked helical virus.

The Baltimore classification sorts viruses into seven groups by the kind of genome they carry and how they turn it into mRNA: double-stranded DNA, single-stranded DNA, double-stranded RNA, positive-sense RNA, negative-sense RNA, and two groups that use reverse transcription. Positive-sense (+) RNA can be read directly by ribosomes; negative-sense (−) RNA is the complement of mRNA and must be copied first.

The enzyme column explains which enzymes appear in a structure diagram. Negative-sense RNA viruses such as influenza must pack their polymerase in the virion, because a host cell has no enzyme that copies RNA from an RNA template. HIV packs reverse transcriptase and integrase for the same reason. Positive-sense viruses such as poliovirus carry no enzyme: their RNA is translated straight away to make one.

Most viruses are 20–300 nm across, roughly 10 to 100 times smaller than a bacterium, and too small to see with a light microscope. OpenStax gives a typical range of about 20 nm to 900 nm, with recently found giant viruses approaching the size of small bacteria. For comparison, an E. coli cell measured by scanning electron microscopy was 1.78 µm long and 0.49 µm wide, and its 70S ribosome is about 21 nm across, almost as big as a poliovirus.

Sizes differ between sources because virions vary from particle to particle and because methods differ: negative-stain electron microscopy dries and flattens particles, while cryo-electron microscopy images them frozen in water. For HIV-1, ViralZone gives 80–100 nm for lentiviruses in general, while cryo-electron tomography of HIV-1 measured 145 ± 25 nm. When a textbook gives one number, treat it as a typical value.

HIV-1 is a roughly spherical enveloped retrovirus. From outside in it has: a lipid envelope carrying Env spikes (gp120 on top of gp41), a matrix layer of p17 under the envelope, a cone-shaped capsid of p24 in the middle, and inside the cone two copies of the single-stranded RNA genome coated with nucleocapsid protein p7, together with the enzymes reverse transcriptase, integrase and protease.

Two numbers make HIV unusual. It carries only about 14 Env spikes per virion, compared with hundreds on an influenza virion, which is thought to help it avoid antibodies. And its mature cores are about 119 nm long and up to 60 nm wide, nearly as long as the virion itself, so the cone sits diagonally across the particle. Switch the viewer to HIV-1 to see the cone inside the cut-away envelope.

Influenza A virus is an enveloped virus, usually rounded and 80–120 nm across, sometimes filamentous. Its envelope carries two spike glycoproteins, hemagglutinin (HA) and neuraminidase (NA), and a few M2 ion channels. The matrix protein M1 lines the envelope, and inside are eight ribonucleoprotein (RNP) segments: negative-sense RNA wrapped around nucleoprotein (NP), each with a polymerase made of PB1, PB2 and PA. The genome totals 13.5 kb.

Segment lengths vary slightly between strains; ViralZone gives a range of 890 to 2,341 nucleotides. The subtype name comes from the spikes: H1N1 carries HA type 1 and NA type 1, H3N2 carries HA 3 and NA 2. So the structure of H1N1 is the structure shown in the model; only the HA and NA proteins differ in sequence. Because the genome is segmented, two influenza strains in one cell can swap segments, which is how new pandemic strains arise.

SARS-CoV-2, the virus that causes COVID-19, is an enveloped, roughly spherical virus about 91 nm across. Its envelope holds three proteins: the large spike (S) glycoprotein, the abundant membrane (M) protein and the small envelope (E) protein. Inside, the nucleocapsid (N) protein packs a single positive-sense RNA genome of about 30 kb, one of the largest of all RNA virus genomes.

In cryo-electron tomograms of intact virions, each particle carried 24 ± 9 spike trimers, which stand on flexible stalks and tilt in different directions. The S1 part of each spike binds the ACE2 receptor on human cells; S2 then drives membrane fusion. The name "corona", crown, comes from the fringe of spikes seen in negative-stain electron micrographs. Choose SARS-CoV-2 in the viewer to see the S, M, E and N proteins.

The infectious hepatitis B virion, called the Dane particle, is an enveloped sphere about 42 nm across. Its envelope carries the surface antigen (HBsAg). Inside is an icosahedral core with T = 4 symmetry, made of core protein (HBcAg), which holds a small, partially double-stranded circular DNA genome of about 3.2 kb and the viral polymerase. Hepatitis B copies its genome through an RNA intermediate, using reverse transcription, which puts it in Baltimore group VII.

The three hepatitis viruses students usually compare are unrelated and built quite differently. Hepatitis A is a small, non-enveloped picornavirus, about 30 nm across, with a pseudo T = 3 capsid and a 7.5 kb positive-sense RNA genome. Hepatitis C is an enveloped virus about 50 nm across, with E1 and E2 glycoproteins and a positive-sense RNA genome of about 10 kb.

Herpesviruses have four layers: a large double-stranded DNA genome, an icosahedral capsid with T = 16 symmetry made of 162 capsomeres, a protein-filled layer called the tegument, and an outer envelope carrying glycoproteins. Herpes simplex virus virions are 150–200 nm across, and the genome is about 152 kb.

The tegument is the feature unique to herpesviruses. Its proteins are delivered into the cell as soon as the envelope fuses, ready to act before any viral gene is switched on. Epstein–Barr virus (EBV) is a herpesvirus with the same layered structure, 150–200 nm across, and a dsDNA genome of about 180 kb according to ViralZone.

Ebola virus is filamentous: long, thread-like virions about 80 nm wide and, on average, about 970 nm long, sometimes branched or curled into a "6" or a loop. It is enveloped, with glycoprotein (GP) spikes, and has a helical nucleocapsid running the length of the filament. The genome is negative-sense RNA of about 18–19 kb that encodes seven proteins.

Tobacco mosaic virus (TMV) is a rigid, non-enveloped helical rod about 300 nm long and 18 nm wide. About 2,130 identical coat-protein subunits stack in a right-handed helix, 16⅓ per turn, and the single positive-sense RNA genome of 6.3–6.5 kb winds between the turns, three nucleotides per subunit. A narrow channel runs down the middle.

TMV was the first virus to be discovered and one of the first whose structure was worked out, and it is the standard example of a helical virus. Its rod builds itself: coat protein forms two-layer disks, the RNA's assembly signal threads into the hole in the middle of a disk, and more protein adds along the RNA until it is fully covered, so the RNA sets the rod's length. In the TMV model, one end is cut open to show the RNA helix inside the protein, and one subunit is highlighted.

Poliovirus is one of the smallest and simplest viruses: a non-enveloped icosahedral particle about 30 nm across. Its capsid has pseudo T = 3 symmetry and is made of 60 protomers, each containing the four proteins VP1, VP2, VP3 and VP4, with VP4 on the inside. It encloses a single positive-sense RNA genome of 7.2–8.5 kb with a small viral protein, VPg, attached to its 5' end instead of a cap. Hepatitis A, rhinoviruses (common cold) and enteroviruses share this design.

Rabies virus is bullet-shaped: an enveloped virion about 180 nm long and 75 nm wide, rounded at one end and flat at the other. Its envelope carries glycoprotein (G) spikes, a matrix protein lies underneath, and inside a helical nucleocapsid of nucleoprotein-coated RNA is coiled tightly to fill the bullet. The genome is negative-sense RNA of about 11 kb, encoding five main proteins.

Measles virus, respiratory syncytial virus (RSV) and Nipah virus are related negative-sense RNA viruses with the same basic plan: a pleomorphic (variably shaped) envelope with two kinds of glycoprotein spike, an attachment protein and a fusion (F) protein, a matrix layer under the envelope, and a long, flexible helical nucleocapsid inside.

Poxviruses are among the largest viruses: brick-shaped particles about 250 nm long and 200 nm wide, big enough to just make out with a good light microscope. The surface is covered with tubules or filaments. Inside is a dumbbell-shaped core holding a linear double-stranded DNA genome of about 170–250 kb, with hairpin ends.

Mpox (monkeypox) virus is an orthopoxvirus, like vaccinia and variola, so it has this same brick-shaped structure. Poxviruses exist in two infectious forms: the intracellular mature virus (one membrane) and the extracellular enveloped virus, which has an extra membrane wrapped around it as it leaves the cell.

Zika and dengue viruses are flaviviruses: small enveloped viruses about 50 nm across with a smooth surface. Instead of sticking out as spikes, the envelope (E) protein lies flat on the membrane, together with the small membrane (M) protein, in an icosahedral-like arrangement. Inside is a single positive-sense RNA genome of 10–11 kb. Immature virions carry the precursor prM instead of M and look spiky until the protein is cut.

Bacteriophages (phages) are viruses that infect bacteria. The best known, phage T4, has a complex structure: an elongated icosahedral head holding double-stranded DNA, a collar, a contractile tail sheath around a hollow tube, a baseplate and six long tail fibres that attach to the bacterium. It injects its DNA rather than entering the cell whole. For a labeled 3D model of T4, see the bacteriophage diagram.

This table compares the structure of the viruses students are most often asked about. Sizes are typical values from ViralZone unless stated; individual particles vary.

Viruses are usually described as non-living, or as being on the border of life. A virus particle has no cells, no ribosomes and no metabolism; it cannot make energy or proteins by itself. OpenStax calls viruses acellular, leaves them out of the tree of life, and describes them as obligate intracellular parasites: they must infect a host cell to reproduce. (OpenStax Microbiology, 6.1 Viruses.)

On the other hand, viruses have genes made of DNA or RNA, those genes mutate, and viruses evolve by natural selection, as the steady arrival of new influenza and SARS-CoV-2 variants shows. Inside an infected cell, a virus redirects the cell's ribosomes and enzymes to make thousands of copies of itself.

A useful way to think about it for an exam: outside a cell, a virion is an inert package, a bit like a seed or a spore but with no metabolism at all. Inside a cell, the virus behaves like a set of instructions that the cell carries out. Whether that counts as alive depends on which definition of life you use. Most biology courses list viruses separately from the living kingdoms for this reason.

Cryo-electron tomography images single frozen virions in 3D, without stain, so it shows how real particles are built rather than an idealised average. For influenza, tomograms of 110 X-31 virions showed that most were spherical, 84 to 170 nm across, and carried about 375 spikes, about six to eight HA for every NA. NA tended to sit in clusters, and the RNPs appeared as rods about 14 nm thick. (Harris et al. (2006), Influenza virus pleiomorphy characterized by cryoelectron tomography, PNAS.)

Electron microscopy of budding influenza particles showed that the eight RNA segments are not packed at random: each particle contains a central rod surrounded by seven others in a reproducible pattern. The 3D model on this page uses that 7 + 1 arrangement. (Noda et al. (2006), Architecture of ribonucleoprotein complexes in influenza A virus particles, Nature.)

HIV-1 is built very differently. Its virions carry only about 14 Env spikes each, far fewer than influenza, and some of them cluster. In the related SIV, the spike's stalk is made of three separate legs, like a tripod. (Zhu et al. (2006), Distribution and three-dimensional structure of AIDS virus envelope spikes, Nature.)

Inside, mature HIV-1 virions averaged 145 ± 25 nm across, and their isolated cores were 119 ± 11 nm long and up to 60 ± 8 nm wide. About a third of virions held two or more cores, and about 7% of cores were tubes rather than cones, so the textbook single cone is the most common form, not the only one. (Briggs et al. (2003), Structural organization of authentic, mature HIV-1 virions and cores, EMBO Journal.)

SARS-CoV-2 virions grown in Vero E6 cells measured 91 ± 11 nm across and carried 24 ± 9 spike trimers each. The spikes stand on flexible stalks and tilt at different angles, and the interior shows granular densities of nucleocapsid protein. (Ke et al. (2020), Structures and distributions of SARS-CoV-2 spike proteins on intact virions, Nature.)

A bacterium is a living prokaryotic cell; a virus is a non-cellular particle that can only reproduce inside a host cell. Bacteria are usually 1–5 µm long, while most viruses are 20–300 nm, small enough that a single bacterium can be infected by hundreds of phages. For the parts of a bacterial cell, see the bacterial cell diagram.

Test yourself: name the eight numbered parts of this enveloped virus, then check the answer key. You can also print the diagram as a virus structure worksheet.

More practice questions, using the 3D models:

1. Which part of an enveloped virus comes from the host cell, and how is it acquired?
2. Name the two spike proteins of influenza A and say what each does.
3. Why must influenza and HIV carry enzymes inside the virion, but poliovirus does not?
4. What is the shape of the HIV capsid, and which protein makes it?
5. How many pentons and hexons does an adenovirus capsid have?
6. Why is tobacco mosaic virus called a helical virus?