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614  structures 93  species 0  interactions 95  sequences 1  architecture

Family: Polyoma_coat (PF00718)

Summary: Polyomavirus coat protein

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This is the Wikipedia entry entitled "Major capsid protein VP1". More...

Major capsid protein VP1 Edit Wikipedia article

Major capsid protein VP1
Mpyv colorbydepth.png
A rendering of an icosahedral viral capsid comprising 72 pentamers of murine polyomavirus VP1, colored such that areas of the surface closer to the interior center appear blue and areas further away appear red. Rendered from PDB: 1SIE​.

Major capsid protein VP1 is a viral protein that is the main component of the polyomavirus capsid. VP1 monomers are generally around 350 amino acids long and are capable of self-assembly into an icosahedral structure consisting of 360 VP1 molecules organized into 72 pentamers. VP1 molecules possess a surface binding site that interacts with sialic acids attached to glycans, including some gangliosides, on the surfaces of cells to initiate the process of viral infection. The VP1 protein, along with capsid components VP2 and VP3, is expressed from the "late region" of the circular viral genome.[1][2][3]


VP1 is the major structural component of the polyomavirus icosahedral capsid, which has T=7 symmetry and a diameter of 40-45 nm. The capsid contains three proteins; VP1 is the primary component and forms a 360-unit outer capsid layer composed of 72 pentamers. The other two components, VP2 and VP3, have high sequence similarity to each other, with VP3 truncated at the N-terminus relative to VP2. VP2 and VP3 assemble inside the capsid in contact with VP1,[1][2] with a stoichiometry of one VP2 or VP3 molecule to each pentamer.[4][5]: 314  VP1 is capable of self-assembly into virus-like particles even in the absence of other viral components.[6] This process requires bound calcium ions and the resulting particles are stabilized by, but do not require, inter-pentamer disulfide bonds.[7]

The structure of an individual pentamer of the murine polyomavirus VP1 protein. Each monomer is colored differently. The conformationally flexible C-terminal arms are shown here in conformations compatible with binding to neighboring molecules. Superposed is a fragment of the polyomavirus VP2 protein (white), which binds to a pentamer oriented toward the central cavity. VP1 is from PDB: 1SIE​; VP2 is from PDB: 1CN3 1CN3​.

The VP1 protein monomer is primarily composed of beta sheets folded into a jelly roll fold. Interactions between VP1 molecules within a pentamer involve extensive binding surfaces, mediated in part by interactions between edge beta-strands. The VP1 C-terminus is disordered and forms interactions between neighboring pentamers in the assembled capsid. The flexibility of the C-terminal arm will enable it to adopt different conformations in the six distinct interaction environments imposed by the symmetry of the icosahedral assembly.[4][8] The C-terminus also contains a basic nuclear localization sequence,[5]: 316  while the N-terminus - which is oriented toward the center of the assembled capsid - contains basic residues that facilitate non-sequence-specific interactions with DNA.[9]

A rendered capsid image with the symmetry-related VP1 monomers shown in different colors and centered on a strict pentamer, producing a radial symmetry effect.
The same capsid structure as above, colored to illustrate the assembly of the icosahedral architecture from VP1 pentamers. Each symmetry-related VP1 monomer is shown in a different color. From PDB: 1SIE​.

Function and trafficking

Murine polyomavirus VP1 in complex with the GT1a glycan. GT1a is shown in yellow and the VP1 monomer with a white surface and a blue protein backbone. A complex network of hydrogen bonds, many water-mediated, is shown at the binding surface by orange lines, with participating protein residues shown as sticks. Mutations of the two residues shown in cyan at the bottom of the figure can significantly affect pathogenicity. From PDB: 5CPW​.[3]

The VP1 protein is responsible for initiating the process of infecting a cell by binding to sialic acids in glycans, including some gangliosides, on the cell surface.[3][8][10] Canonically, VP1 interacts specifically with α(2,3)-linked and α(2,6)-linked sialic acids.[3][8] In some cases additional factors are necessary conditions for viral entry; for example, JC virus requires the 5HT2A serotonin receptor for entry, although the specific mechanism of this requirement is unclear.[11] Once attached to the cell surface, the virions enter the cell and are trafficked by a retrograde pathway to the endoplasmic reticulum. The exact mechanism of endocytosis varies depending on the virus, and some viruses use multiple mechanisms; caveolae-dependent mechanisms are common.[12] The process by which polyomaviruses penetrate the membrane and exit the ER is not well understood, but conformational changes to VP1, possibly including reduction of its disulfide bonds, likely occur in the ER. For some polyomaviruses, VP1 has been detected reaching the nucleus along with the viral genome, though it is unclear how the genomic DNA disengages from VP1.[12]

All of the capsid proteins are expressed from the late region of the viral genome, so named because expression occurs only late in the infection process. VP1 has a nuclear localization sequence that enables import from the cytoplasm where it is synthesized by the host translation machinery to the cell nucleus where new virions are assembled. This nuclear import process, mediated by karyopherins, acts on assembled VP1 pentamers in complex with VP2 or VP3; oligomerization to form capsids occurs in the nucleus.[5]: 316–17 


  1. ^ a b Ramqvist T, Dalianis T (August 2009). "Murine polyomavirus tumour specific transplantation antigens and viral persistence in relation to the immune response, and tumour development". Seminars in Cancer Biology. 19 (4): 236–43. doi:10.1016/j.semcancer.2009.02.001. PMID 19505651.
  2. ^ a b Ramqvist T, Dalianis T (February 2010). "Lessons from immune responses and vaccines against murine polyomavirus infection and polyomavirus-induced tumours potentially useful for studies on human polyomaviruses". Anticancer Research. 30 (2): 279–84. PMID 20332429.
  3. ^ a b c d Buch MH, Liaci AM, O'Hara SD, Garcea RL, Neu U, Stehle T (October 2015). "Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity". PLoS Pathogens. 11 (10): e1005104. doi:10.1371/journal.ppat.1005104. PMC 4608799. PMID 26474293.
  4. ^ a b Chen XS, Stehle T, Harrison SC (June 1998). "Interaction of polyomavirus internal protein VP2 with the major capsid protein VP1 and implications for participation of VP2 in viral entry". The EMBO Journal. 17 (12): 3233–40. doi:10.1093/emboj/17.12.3233. PMC 1170661. PMID 9628860.
  5. ^ a b c Almendral, José M. (2013). "Assembly of Simple Icosahedral Viruses". In Mateu, Mauricio G. (ed.). Structure and physics of viruses an integrated textbook. Dordrecht: Springer. ISBN 978-94-007-6552-8.
  6. ^ Salunke DM, Caspar DL, Garcea RL (September 1986). "Self-assembly of purified polyomavirus capsid protein VP1". Cell. 46 (6): 895–904. doi:10.1016/0092-8674(86)90071-1. PMID 3019556.
  7. ^ Schmidt U, Rudolph R, Böhm G (February 2000). "Mechanism of assembly of recombinant murine polyomavirus-like particles". Journal of Virology. 74 (4): 1658–62. doi:10.1128/jvi.74.4.1658-1662.2000. PMC 111640. PMID 10644335.
  8. ^ a b c Stehle T, Harrison SC (February 1996). "Crystal structures of murine polyomavirus in complex with straight-chain and branched-chain sialyloligosaccharide receptor fragments". Structure. 4 (2): 183–94. doi:10.1016/s0969-2126(96)00021-4. PMID 8805524.
  9. ^ Moreland RB, Montross L, Garcea RL (March 1991). "Characterization of the DNA-binding properties of the polyomavirus capsid protein VP1". Journal of Virology. 65 (3): 1168–76. PMC 239883. PMID 1847446.
  10. ^ Tsai B, Gilbert JM, Stehle T, Lencer W, Benjamin TL, Rapoport TA (September 2003). "Gangliosides are receptors for murine polyoma virus and SV40". The EMBO Journal. 22 (17): 4346–55. doi:10.1093/emboj/cdg439. PMC 202381. PMID 12941687.
  11. ^ Maginnis MS, Nelson CD, Atwood WJ (December 2015). "JC polyomavirus attachment, entry, and trafficking: unlocking the keys to a fatal infection". Journal of Neurovirology. 21 (6): 601–13. doi:10.1007/s13365-014-0272-4. PMC 4312552. PMID 25078361.
  12. ^ a b Tsai B, Qian M (2010). "Cellular entry of polyomaviruses". Current Topics in Microbiology and Immunology. 343: 177–94. doi:10.1007/82_2010_38. PMID 20373089.

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Polyomavirus coat protein Provide feedback

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This tab holds annotation information from the InterPro database.

InterPro entry IPR000662

This entry represents the major capsid protein VP1 (viral protein 1) from Polyomaviruses, such as Murine polyomavirus (strain P16 small-plaque) (MPyV) [ PUBMED:9628860 ]. Polyomaviruses are dsDNA viruses with no RNA stage in their life cycle. The virus capsid is composed of 72 icosahedral units, each of which is composed of five copies of VP1. The virus attaches to the cell surface by recognition of oligosaccharides terminating in alpha(2,3)-linked sialic acid. The capsid protein VP1 forms a pentamer. The complete capsid is composed of 72 VP1 pentamers, with a minor capsid protein, VP2 or VP3, inserted into the centre of each pentamer like a hairpin. This structure restricts the exposure of internal proteins during viral entry. Polyomavirus coat assembly is rigorously controlled by chaperone-mediated assembly. During viral infection, the heat shock chaperone hsc70 binds VP1 and co-localises it in the nucleus, thereby regulating capsid assembly [ PUBMED:12928495 ].

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Seed source: Pfam-B_748 (release 2.1)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 1
Number in full: 95
Average length of the domain: 290.50 aa
Average identity of full alignment: 49 %
Average coverage of the sequence by the domain: 76.69 %

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HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 34.2 30.6
Noise cut-off 25.7 25.2
Model length: 293
Family (HMM) version: 23
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Polyoma_coat domain has been found. There are 614 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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