Virus Assembly


Viral genomes are sequestered by capsid proteins to form nucleocapsids with icosahedral (pseudospherical) or helical symmetry. Mature virus particles (virions) may be naked (i.e. composed of nucleic acid and protein only) or enveloped within a lipid bilayer(s). There is great diversity in size and complexity across the virus spectrum; recently discovered giant viruses are larger than some bacteria. Virions assemble from relatively large numbers of a few identical subunits but may include additional proteins required for specialised functions. Various mechanisms ensure that only viral genomic nucleic acids are packaged. Virion components are transported by cellular processes to sites of assembly. Basic functions of virions are protection of the genome from environmental damage during extracellular existence and delivery to a susceptible cell to initiate a new infection. Proteolytic cleavage of specific proteins during virus maturation commonly induces a quasi‐stable ‘triggered’ state to allow conformational changes necessary for cell penetration and genome release.

Key Concepts

  • For genetic economy, virions are assembled from large numbers of a few components.
  • Nucleocapsids comprise the viral genomic nucleic acid sequestered within a protein coat.
  • The symmetry of nucleocapsids is usually icosahedral or helical.
  • Virions are either nonenveloped (i.e. a naked nucleocapsid) or enveloped by a lipid membrane.
  • Virus‐specific nucleic acids are selectively packaged within nucleocapsids.
  • Intracellular transport mechanisms are hijacked by viruses to ensure that components are delivered to sites of assembly.
  • Postassembly proteolytic cleavages are often used to induce a quasi‐stable state primed for cell entry.

Keywords: nucleocapsid; envelope; icosahedral; helical; packaging signals; intracellular transport; maturation

Figure 1. Virus gallery: A range of viruses are illustrated differing in their capsid architectures and their genome types. (a) Electron micrograph of TMV, the classical helical virus; (b) examples of spherical viruses with icosahedral capsids with differing triangulation numbers (Reproduced with permission from Fontana and Steven (2015) © Elsevier.); (c) viruses known to assemble using multiple RNA‐based PSs, STNV (left) and bacteriophage MS2 (right), see Figure; (d) the large (T = 25) bacteriophage PRD1 showing a front view with its major CPs removed to highlight the roles of ‘ruler’ proteins, shown as extended chains, to define the locations of its symmetry axes. PRD1 also encompasses a membrane bilayer (yellow/orange layers), as seen in the adjacent cross section (Reproduced with permission from Cockburn et al. (2004) © Dr Joseph Cockburn, Leeds/Nature Publishing Group.); (e) Top – cartoon of the mature HIV nucleocapsid, which has the geometry of a fullerene cone. The latter is a closed structure composed of hexameric and pentameric assemblies. Closure, as with icosahedral particles, requires that it contains 12 fivefold capsomeres, highlighted in red. The asymmetry is generated by the large end having 7/12 fivefolds. Bottom – cryo‐EM images of HIV infected cells showing the formation of the Fullerene cone as the particles mature (i–iii) (Reproduced from Briggs et al. (2006) © Elsevier.). False colour is added in (iii) to ease interpretation.
Figure 2. Molecular mechanisms of packaging signal‐mediated assembly: (a) Mechanism of TMV assembly. A self‐assembled two‐layer symmetrical disk of the CP interacts with a specific sequence within the TMV genome leading to dislocation of the disk into the assembly‐competent ‘lock washer’ with growth points at both ends. Simultaneously, the RNA assembly initiation site structure is denatured allowing each CP to contact three nucleotides along the central pore of the virion. As the initiation site is internal within the genome, this creates assembly intermediates in which both RNA ends enter the growing helical rod from the same end. The red cartoons to the right of the assembly intermediates illustrate the presumed RNA structures present during these steps. (b) An illustration of the packaging problems faced by ssRNA spherical viruses. The RNA shown below the cartoon of the capsid into which it is packaged is drawn roughly to scale. (c) A solution to the challenge shown in (b) is the presence of multiple PSs distributed throughout viral genomes. For MS2, a T = 3 virion composed of 180 CP subunits organised as two types of noncovalent dimer, 60 A/B and 30 C/C. PS–CP interactions regulate the conformation of the dimeric capsomere during assembly favouring the A/B conformer. Both types of dimers are required for higher order assembly of intermediates on the pathway to complete the capsid. The CPs are shown as ribbon diagrams, while the highest affinity PS, a 19‐nt stem‐loop is shown as a framework structure. Crosslinking of the CPs and genomic RNA in infectious virions confirms that this mechanism is used in vivo. (d) The same PS‐mediated mechanism occurs for assembly of the T = 1 STNV, a virus having a CP with a canonical ‘jelly roll’ globular domain with a positively charged N‐terminal arm. There is no need to define the CP conformer in this case because all 60 CPs in the capsid are identical. Capsid assembly is still dependent on binding PSs. The CP recognition sequences (highlighted in red in the loops) and relative placement of PS sites, like the five predicted to occur in the 5′ 127 nts genomic segment illustrated, promote cooperative assembly while neutralising electrostatic repulsions between the N termini of the CP monomers, allowing a trimer capsomere to form. (e) Left: The X‐ray structure of an STNV T = 1 virus‐like particle (PDB 2BUK), assembled around one of its PS RNAs, viewed along a twofold axis. Right: Ribbon diagram of the STNV CP subunit structure seen in virions (PDB 3S4G) with the disordered N‐terminal amino acid sequence shown dashed, with the sequence of the first 25 amino acids below. When this assembles around a PS RNA, there is additional ordering of the CP N‐terminal region (magenta helical turn) in response to binding the preferred RNA sequence.
Figure 3. Hepatitis B core: An example of a VLP: (a) Ribbon diagram of the assembled HBc particle showing the prominent surface ‘spikes’ formed from coat protein dimers. (b) Structural dimer of the HBc protein. MIR is the major immunogenic region preferred for antigen insertion. Linker is a sequence replacing the C‐terminal domain of an upstream HBc protein and linking it to the N terminus of a downstream copy, thus defining the HBc protein dimer association. Reproduced from Peyret et al. (2015) © Creative Commons Attribution (CC BY) license.
Figure 4. Examples of proteolytic cleavages associated with viral maturation: (a) Conversion of the herpesvirus procapsid into the DNA‐filled C‐capsid involves the cleavage and release of proteins forming the assembly scaffold and filling of the internal space with DNA via the pore and motor indicated by UL6. (Reproduced from Trus et al. () © Cell Press (Elsevier).). (b) Maturation cleavage of VP0 in poliovirus allows the rearrangement of the VP4 component to form an internal stabilising network on the inner surface of the virion. On the left is a stereo view from the inside of the capsid fivefold axis, showing the overlay of VP4 (red) and the first 78 residues of VP0 (blue). The scission point on VP0 is marked with a yellow sphere (arrowed). The remaining capsid proteins are shown in grey for context. On the right is an overlay of the crystal structures of VP0 (blue) and VP4, and the first few residues of VP2 (Red) show the difference between the two structures. The scission site (yellow sphere) at residue 69 of VP0 extends farther from the fivefold axis in the native (cleaved) structure. Paler‐coloured ribbons of the neighbouring symmetry copies of VP0 and VP4 are shown for context (Courtesy of J. Hogle and M. Strauss.). (c) Cleavage of HA0, the precursor to the influenza receptor‐binding glycoprotein, into HA1 and HA2 allows the molecule to undergo the massive conformational changes induced by reduction in pH that are necessary for fusion with the cell membrane during cell entry. Note: only HA2 is shown in the acid‐induced form for clarity. Courtesy of I. Wilson and P. Lee.
Figure 5. Acquisition of membranes and intracellular transport as exemplified by the herpesviruses: (a) Herpesvirus capsids assemble and mature in the nucleus and then bud through first the inner nuclear membrane and then the outer nuclear membrane, first gaining and then shedding a membrane in the process. (b) The glycoproteins present at the surface of mature herpesvirus particles are synthesised in the endoplasmic reticulum (ER) and transported to the plasma membrane via the Golgi apparatus (GA) and trans‐Golgi network (TGN). They are then internalised in early endosomes (EE) where they associate with c‐capsids together with tegument protein. These bud into the endosomes to form mature enveloped particles which are transported to the cell surface and released via the recycling endosome route. Reproduced from Hollinshead et al. (2012)© European Molecular Biology Organization.


Abrescia NG, Cockburn JJ, Grimes JM, et al. (2004) Insights into assembly from structural analysis of bacteriophage PRD1. Nature 432: 68–74.

Anzola JV, Xu ZK, Asamizu T and Nuss DL (1987) Segment‐specific inverted repeats found adjacent to conserved terminal sequences in wound tumor virus genome and defective interfering RNAs. Proceedings of the National Academy of Sciences 84: 8301–8305.

Baines JD (2011) Herpes simplex virus capsid assembly and DNA packaging: a present and future antiviral drug target. Trends in Microbiology 19: 606–613. DOI: 10.1016/j.tim.2011.09.001.

Bakker SE, Ford RJ, Barker AM, et al. (2012) Isolation of an asymmetric RNA uncoating intermediate for a single‐stranded RNA plant virus. Journal of Molecular Biology 417: 65–78. DOI: 10.1016/j.jmb.2012.01.017.

Bancroft JB (1970) The self‐assembly of spherical plant viruses. Advances in Virus Research 16: 99–134.

Basavappa R, Syed R, Flore O, et al (1994) Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: structure of the empty capsid assembly intermediate at 2.9 A resolution. Protein Science 3: 1651–1669. DOI: 10.1002/pro.5560031005.

Belyi VA and Muthukumar M (2006) Electrostatic origin of the genome packing in viruses. Proceedings of the National Academy of Sciences 103: 17174–17178. DOI: 10.1073/pnas.0608311103.

Borodavka A, Tuma R and Stockley PG (2012) Evidence that viral RNAs have evolved for efficient, two‐stage packaging. Proceedings of the National Academy of Sciences of the United States of America 109: 15769–15774. DOI: 10.1073/pnas.1204357109.

Borodavka A, Tuma R and Stockley PG (2013) A two‐stage mechanism of viral RNA compaction revealed by single molecule fluorescence. RNA Biology 10: 481–489. DOI: 10.4161/rna.23838.

Briggs JAG, Grünewald K, Glass B, et al (2006) The mechanism of HIV‐1 core assembly: insights from three‐dimensional reconstructions of authentic virions. Structure 14: 15–20. DOI: 10.1016/j.str.2005.09.010.

Bunka DHJ, Lane SW, Lane CL, et al (2011) Degenerate RNA packaging signals in the genome of Satellite Tobacco Necrosis Virus: implications for the assembly of a T = 1 capsid. Journal of Molecular Biology 413: 51–65. DOI: 10.1016/j.jmb.2011.07.063.

Caspar DL and Klug A (1962) Physical principles in the construction of regular viruses. Cold Spring Harbor Symposia on Quantitative Biology 27: 1–24.

Cockburn JJB, Abrescia NGA, Grimes JM, et al (2004) Membrane structure and interactions with protein and DNA in bacteriophage PRD1. Nature 432: 122–125. DOI: 10.1038/nature03053.

Crick FH and Watson JD (1956) Structure of small viruses. Nature 177: 473–475.

Danthi P, Holm GH, Stehle T and Dermody TS (2013) Reovirus receptors, cell entry, and proapoptotic signaling. Advances in Experimental Medicine and Biology 790: 42–71. DOI: 10.1007/978-1-4614-7651-1_3.

Dykeman EC, Stockley PG and Twarock R (2014) Solving a Levinthal's paradox for virus assembly identifies a unique antiviral strategy. Proceedings of the National Academy of Sciences of the United States of America 111: 5361–5366. DOI: 10.1073/pnas.1319479111.

Feng Z, Hensley L, McKnight KL, et al (2013) A pathogenic picornavirus acquires an envelope by hijacking cellular membranes. Nature 496: 367–371.

Fontana J and Steven AC (2015) Influenza virus‐mediated membrane fusion: structural insights from electron microscopy. Archives of Biochemistry and Biophysics. DOI: 10.1016/

Gelbart WM and Knobler CM (2009) Virology. Pressurized viruses. Science 323: 1682–1683. DOI: 10.1126/science.1170645.

Geller R, Vignuzzi M, Andino R and Frydman J (2007) Evolutionary constraints on chaperone‐mediated folding provide an antiviral approach refractory to development of drug resistance. Genes and Development 21: 195–205. DOI: 10.1101/gad.1505307.

Gilbert RJ, Beales L, Blond D, et al (2005) Hepatitis B small surface antigen particles are octahedral. Proceedings of the National Academy of Sciences 102: 14783–14788.

Gopal A, Egecioglu DE, Yoffe AM, et al (2014) Viral RNAs are unusually compact. PLoS One 9: e105875. DOI: 10.1371/journal.pone.0105875.

Goto H, Muramoto Y, Noda T and Kawaoka Y (2013) The genome‐packaging signal of the influenza A virus genome comprises a genome incorporation signal and a genome‐bundling signal. Journal of Virology 87: 11316–11322.

Harrison SC, Olson AJ, Schutt CE, et al (1978) Tomato bushy stunt virus at 2.9 A resolution. Nature 276: 368–373. DOI: 10.1038/276368a0.

Hollinshead M, Johns HL, Sayers CL, et al (2012) Endocytic tubules regulated by Rab GTPases 5 and 11 are used for envelopment of herpes simplex virus. EMBO Journal 31: 4204–4220. DOI: 10.1038/emboj.2012.262.

Kielian M and Rey FA (2006) Virus membrane‐fusion proteins: more than one way to make a hairpin. Nature Reviews. Microbiology 4: 67–76.

Kim DY, Firth AE, Atasheva S, et al (2011) Conservation of a packaging signal and the viral genome RNA packaging mechanism in alphavirus evolution. Journal of Virology 85: 8022–8036. DOI: 10.1128/JVI.00644-11.

Klug A (1999) The tobacco mosaic virus particle: structure and assembly. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 354: 531–535. DOI: 10.1098/rstb.1999.0404.

Kutluay SB, Zang T, Blanco‐Melo D, et al (2014) Global changes in the RNA binding specificity of HIV‐1 gag regulate virion genesis. Cell 159: 1096–1109. DOI: 10.1016/j.cell.2014.09.057.

Lu X, McDonald SM, Tortorici MA, et al (2008) Mechanism for coordinated RNA packaging and genome replication by rotavirus polymerase VP1. Structure 16: 1678–1688. DOI: 10.1016/j.str.2008.09.006.

Meng B and Lever AM (2013) Wrapping up the bad news: HIV assembly and release. Retrovirology 10: 5.

Namba K, Pattanayek R and Stubbs G (1989) Visualization of protein‐nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X‐ray fiber diffraction. Journal of Molecular Biology 208: 307–325.

Nemecek D, Cheng N, Qiao J and Mindich L (2011) Stepwise expansion of the bacteriophage φ6 procapsid: possible packaging intermediates. Journal of Molecular Biology 414: 260–271. DOI: 10.1016/j.jmb.2011.10.004.

Patel N, Dykeman EC, Coutts RHA, et al (2015) Revealing the density of encoded functions in a viral RNA. Proceedings of the National Academy of Sciences 112: 2227–2232. DOI: 10.1073/pnas.1420812112.

Peyret H, Gehin A, Thuenemann EC, et al (2015) Tandem fusion of hepatitis B core antigen allows assembly of virus‐like particles in bacteria and plants with enhanced capacity to accommodate foreign proteins. PLoS One 10 (4): e0120751.

Poranen MM and Tuma R (2004) Self‐assembly of double‐stranded RNA bacteriophages. Virus Research 101: 93–100.

Prasad BVV and Schmid MF (2012) Principles of virus structural organization. In: Viral Molecular Machines, pp. 17–47. Boston, MA: Springer.

Pumpens P and Grens E (2001) HBV core particles as a carrier for B cell/T cell epitopes. Intervirology 44: 98–114.

Qu F and Morris TJ (1997) Encapsidation of turnip crinkle virus is defined by a specific packaging signal and RNA size. Journal of Virology 71: 1428–1435.

Romero‐Brey I, Merz A, Chiramel A, et al (2012) Three‐dimensional architecture and biogenesis of membrane structures associated with hepatitis C virus replication. PLoS Pathogens 8: e1003056. DOI: 10.1371/journal.ppat.1003056.

Routh A, Domitrovic T and Johnson JE (2012) Host RNAs, including transposons, are encapsidated by a eukaryotic single‐stranded RNA virus. Proceedings of the National Academy of Sciences of the United States of America 109: 1907–1912. DOI: 10.1073/pnas.1116168109.

San Martin C (2012) Latest insights on adenovirus structure and assembly. Viruses 4: 847–877.

Schiller JT and Müller M (2015) Next generation prophylactic human papillomavirus vaccines. Lancet Oncology 16: e217–e225. DOI: 10.1016/S1470-2045(14)71179-9.

van der Schoot P and Bruinsma R (2005) Electrostatics and the assembly of an RNA virus. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics 71: 061928.

Smith G (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228: 1315–1317. DOI: 10.1126/science.4001944.

Sugrue RJ and Hay AJ (1991) Structural characteristics of the M2 protein of influenza A viruses: evidence that it forms a tetrameric channel. Virology 180: 617–624.

Sun S, Kondabagil K, Draper B, et al (2008) The structure of the phage T4 DNA packaging motor suggests a mechanism dependent on electrostatic forces. Cell 135: 1251–1262. DOI: 10.1016/j.cell.2008.11.015.

Sun S, Rao VB and Rossmann MG (2010) Genome packaging in viruses. Current Opinion in Structural Biology 20: 114–120. DOI: 10.1016/

Toropova K, Basnak G, Twarock R, et al (2008) The three‐dimensional structure of genomic RNA in bacteriophage MS2: implications for assembly. Journal of Molecular Biology 375: 824–836. DOI: 10.1016/j.jmb.2007.08.067.

Trask SD, McDonald SM and Patton JT (2012) Structural insights into the coupling of virion assembly and rotavirus replication. Nature Reviews. Microbiology 10: 165–177. DOI: 10.1038/nrmicro2673.

Trus BL, Newcomb WW, Cheng N, et al (2007) Allosteric signaling and a nuclear exit strategy: binding of UL25/UL17 heterodimers to DNA‐filled HSV‐1 capsids. Molecular Cell 26: 479–489. DOI: 10.1016/j.molcel.2007.04.010.

Turner DR, Joyce LE and Butler PJ (1988) The tobacco mosaic virus assembly origin RNA. Functional characteristics defined by directed mutagenesis. Journal of Molecular Biology 203: 531–547.

Tuthill TJ, Bubeck D, Rowlands DJ and Hogel JM (2006) Characterization of early steps in the poliovirus infection process: receptor‐decorated liposomes induce conversion of the virus to membrane‐anchored entry‐intermediate particles. Journal of Virology 80: 172–180.

Valenzuela P, Medina A, Rutter WJ, et al (1982) Synthesis and assembly of hepatitis B virus surface antigen particles in yeast. Nature 298: 347–350.

Wang Q, Lin T, Tang L, et al (2002) Icosahedral virus particles as addressable nanoscale building blocks. Angewandte Chemie 41: 459–462.

Wickner W (1988) Mechanisms of membrane assembly: general lessons from the study of M13 coat protein and Escherichia coli leader peptidase. Biochemistry 27: 1081–1086.

Further Reading

Ganser BK (1999) Assembly and Analysis of Conical Models for the HIV‐1 Core. Science 283: 80–83. DOI: 10.1126/science.283.5398.80.

Khudyakov Y and Pumpens P (eds) (2015) Viral Nanotechnology. CRC Press Print. ISBN: 978-1-4664-8352-8. eBook ISBN: 978-1-4665-8353-5.

Rossmann MG and Rao VB (eds) (2012) Viral Molecular Machines (Advances in Experimental Medicine and Biology, vol. 726). New York: Springer.

Steinmetz NF and Manchester M (2011) Viral Nanoparticles: Tools for Materials Science & Biomedicine. Singapore: Pan Stanford Publishing Pte Ltd.

Stockley PG and Twarock R (eds) (2010) Emerging Techniques in Physical Virology. London: Imperial College Press.

Virus Assembly (2013) Eric Hunter. In: Knipe DM, Howley PM, et al. (eds) Fields Virology, 6th edn. Philadelphia, PA: Lippincott‐Raven.

Zlotnick A (2004) Viruses and the physics of soft condensed matter. Proceedings of the National Academy of Sciences 101: 15549–15550. DOI: 10.1073/pnas.0406935101.

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Rowlands, David J, and Stockley, Peter G(Jun 2016) Virus Assembly. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0024782]