Summary: Polyomavirus coat protein
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This is the Wikipedia entry entitled "Major capsid protein VP1". More...
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Major capsid protein VP1 Edit Wikipedia article
|Major capsid protein VP1|
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.
VP1 is the major structural component of the polyomavirus icosahedral capsid, which has T=7 symmetry and a diameter of 40-45Â 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, with a stoichiometry of one VP2 or VP3 molecule to each pentamer.:â€Š314â€Š VP1 is capable of self-assembly into virus-like particles even in the absence of other viral components. This process requires bound calcium ions and the resulting particles are stabilized by, but do not require, inter-pentamer disulfide bonds.
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. The C-terminus also contains a basic nuclear localization sequence,:â€Š316â€Š 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.
Function and trafficking
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. Canonically, VP1 interacts specifically with Î±(2,3)-linked and Î±(2,6)-linked sialic acids. 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. 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. 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.
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.:â€Š316â€“17â€Š
- 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): 236â€“43. doi:10.1016/j.semcancer.2009.02.001. PMIDÂ 19505651.
- 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): 279â€“84. PMIDÂ 20332429.
- 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. PMCÂ 4608799. PMIDÂ 26474293.
- 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): 3233â€“40. doi:10.1093/emboj/17.12.3233. PMCÂ 1170661. PMIDÂ 9628860.
- Almendral, JosÃ© M. (2013). "Assembly of Simple Icosahedral Viruses". In Mateu, Mauricio G. (ed.). Structure and physics of viruses an integrated textbook. Dordrecht: Springer. ISBNÂ 978-94-007-6552-8.
- Salunke DM, Caspar DL, Garcea RL (September 1986). "Self-assembly of purified polyomavirus capsid protein VP1". Cell. 46 (6): 895â€“904. doi:10.1016/0092-8674(86)90071-1. PMIDÂ 3019556.
- Schmidt U, Rudolph R, BÃ¶hm G (February 2000). "Mechanism of assembly of recombinant murine polyomavirus-like particles". Journal of Virology. 74 (4): 1658â€“62. doi:10.1128/jvi.74.4.1658-1662.2000. PMCÂ 111640. PMIDÂ 10644335.
- 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): 183â€“94. doi:10.1016/s0969-2126(96)00021-4. PMIDÂ 8805524.
- 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): 1168â€“76. PMCÂ 239883. PMIDÂ 1847446.
- 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): 4346â€“55. doi:10.1093/emboj/cdg439. PMCÂ 202381. PMIDÂ 12941687.
- 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): 601â€“13. doi:10.1007/s13365-014-0272-4. PMCÂ 4312552. PMIDÂ 25078361.
- Tsai B, Qian M (2010). "Cellular entry of polyomaviruses". Current Topics in Microbiology and Immunology. 343: 177â€“94. doi:10.1007/82_2010_38. PMIDÂ 20373089.
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External database links
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 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||viral capsid (GO:0019028)|
|Molecular function||structural molecule activity (GO:0005198)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This large superfamily includes nucleoplasmin as well as a wide range of viral coat and capsid proteins that share a jelly roll topology.
The clan contains the following 42 members:Adeno_hexon_C Astro_capsid_N Birna_VP2 Bromo_coat Calici_coat Calici_coat_C Capsid-VNN Capsid_N Carmo_coat_C Circo_capsid Como_LCP Como_SCP CRPV_capsid Cucumo_coat Dicistro_VP4 DUF2961 DUF4621 HAV_VP IHHNV_capsid Ilar_coat Late_protein_L1 Luteo_coat Nepo_coat Nepo_coat_C Nepo_coat_N NPL Nucleoplasmin Peptidase_A21 Peptidase_A6 Pico_P1A Polyhedrin Polyoma_coat Pox_Rif Rhv SP2 TGFb_propeptide TNV_CP TT_ORF1 Tymo_coat Viral_coat VP4_2 Waikav_capsid_1
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
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|Seed source:||Pfam-B_748 (release 2.1)|
|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 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||23|
|Download:||download the raw HMM for this family|
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How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
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Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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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