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Hoffmann, R. A wiki for the life sciences where authorship matters. Nature Genetics (2008)
MeSH Review


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Disease relevance of Capsid

  • Cyclophilin A subsequently performs an essential function in HIV-1 replication, possibly helping to disassemble the capsid core upon infection [1].
  • The capsid shells of bacteriophage HK97 and several other phages contain polypeptides that are covalently linked into complexes so large that they do not enter polyacrylamide gels after denaturation [2].
  • The polyomavirus capsid is built from 72 pentamers of VP1 that form three different types of connections in the T = 7d icosahedral surface lattice [3].
  • Analogies with other myristylated proteins suggest that the myristate moiety in picornaviruses may be involved in capsid assembly or in the entry of virus into cells [4].
  • The L1 and L2 proteins form icosahedral capsids for progeny virion generation [5].

High impact information on Capsid

  • The hexameric ATPase P4 of dsRNA bacteriophage phi12, located at the vertices of the icosahedral capsid, is such a packaging motor [6].
  • The reovirus polymerase and those of other dsRNA viruses function within the confines of a protein capsid to transcribe the tightly packed dsRNA genome segments [7].
  • We report the 2.36 A crystal structure of the N-terminal domain of HIV-1 capsid (residues 1-151) in complex with human cyclophilin A. A single exposed capsid loop (residues 85-93) binds in the enzyme's active site, and Pro-90 adopts an unprecedented trans conformation [1].
  • The fibers are released, the penton base structures dissociated, the proteins connecting the DNA to the inside surface of the capsid degraded or shed, and the capsid-stabilizing minor proteins eliminated [8].
  • The empty capsid structure has only one layer which is indistinguishable from the outer layer of the full capsids [9].

Chemical compound and disease context of Capsid

  • Conditions have been found under which more than 95% of the major head protein (P23) undergoes the same cleavage that occurs during development of the normal capsid [10].
  • The C-terminal tryptophan remains in the P1 substrate site subsequent to the autocatalytic cis cleavage of the capsid protein, thus rendering the proteinase inactive [11].
  • In our original crystal structure of FMDV the Arg-Gly-Asp-containing loop ('the loop'), located between beta-strands G and H of capsid protein VP1, was disordered and hence essentially invisible [12].
  • In each of the major capsid proteins, the "connecting loops" and NH2- and COOH-terminal extensions are structurally dissimilar [13].
  • Two major cellular defenses against infection by retroviruses are the Fv1 and TRIM5 class of inhibitors that target incoming retroviral capsids and the APOBEC3 class of cytidine deaminases that hypermutate and destabilize retroviral genomes [14].

Biological context of Capsid

  • The mammalian reovirus haemagglutinin (sigma 1 protein), which is an outer capsid protein, has been shown to be a major factor in determining virus-host cell interactions [15].
  • A polymerase chain reaction method involving use of degenerate oligonucleotide primers, in which the conserved region of the open reading frame of the HPV L1 (major capsid protein) gene is amplified, was used to amplify total cellular DNA purified from individual tumors [16].
  • Comparison of the amino acid sequence of the capsid protein with that of serine proteases leads us to hypothesize that histidine-141, aspartate-147, and serine-215 of the Sindbis capsid protein form the catalytic triad of a serine protease [17].
  • Resulting recombinant plasmid pSW119 expressed in Escherichia coli a VP1-beta-lactamase fusion protein that reacted with antibodies raised against poliovirus capsid polypeptide VP1 and with a monoclonal poliovirus type 1 neutralizing antibody, C3 [18].
  • In this report, we constructed a phylogenetic tree for 14 isolates (7 archetypes and 7 PML types) from DNA sequence data on the VP1 (major capsid protein) gene [19].

Anatomical context of Capsid

  • Using quantitative biochemical, immunochemical and morphological methods, we demonstrate that inhibitors of the cystine protease, L3/p23, located inside the capsid block the degradation of the capsid-stabilizing protein VI, and prevent virus uncoating at the nuclear membrane [20].
  • A domain of SV40 capsid polypeptide VP1 that specifies migration into the cell nucleus [21].
  • Rotavirus assembles in the rough endoplasmic reticulum (RER) and encodes two glycoproteins: VP7, a component of the outer viral capsid, and NCVP5, a nonstructural protein [22].
  • The virus-producing cell line P3HRF-1 consistently shows reduced viral genome numbers and viral capsid antigen on prolonged exposure to acyclovir [23].
  • After infection, the expression of a restricting TRIM5alpha in the target cells correlated with a decrease in the amount of particulate capsid in the cytosol [24].

Gene context of Capsid

  • Cyclophilin A could then function by weakening the association between capsid strips, thereby promoting disassembly of the viral core [1].
  • Genetic evidence implicates a direct interaction between the Fv1 gene product and a component of the viral preintegration complex, the capsid protein CA (refs 7-9) [25].
  • Gene 69 is bracketed by the non-essential early gene dam (DNA adenine methylase) and the late gene soc (small outer capsid protein) [26].
  • By using a panel of MLV capsid mutants, subtle differences in the anti-MLV activity were identified among the different primate Trim5alpha cDNAs [27].
  • TAg and capsid protein expressions, as well as increased p53 and nuclear beta-catenin, were observed between T0 and T7 for Mad-1 and Delta98 alone [28].

Analytical, diagnostic and therapeutic context of Capsid


  1. Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV-1 capsid. Gamble, T.R., Vajdos, F.F., Yoo, S., Worthylake, D.K., Houseweart, M., Sundquist, W.I., Hill, C.P. Cell (1996) [Pubmed]
  2. Protein chainmail: catenated protein in viral capsids. Duda, R.L. Cell (1998) [Pubmed]
  3. Inside polyomavirus at 25-A resolution. Griffith, J.P., Griffith, D.L., Rayment, I., Murakami, W.T., Caspar, D.L. Nature (1992) [Pubmed]
  4. Myristylation of picornavirus capsid protein VP4 and its structural significance. Chow, M., Newman, J.F., Filman, D., Hogle, J.M., Rowlands, D.J., Brown, F. Nature (1987) [Pubmed]
  5. Pathogenesis of human papillomaviruses in differentiating epithelia. Longworth, M.S., Laimins, L.A. Microbiol. Mol. Biol. Rev. (2004) [Pubmed]
  6. Atomic snapshots of an RNA packaging motor reveal conformational changes linking ATP hydrolysis to RNA translocation. Mancini, E.J., Kainov, D.E., Grimes, J.M., Tuma, R., Bamford, D.H., Stuart, D.I. Cell (2004) [Pubmed]
  7. RNA synthesis in a cage--structural studies of reovirus polymerase lambda3. Tao, Y., Farsetta, D.L., Nibert, M.L., Harrison, S.C. Cell (2002) [Pubmed]
  8. Stepwise dismantling of adenovirus 2 during entry into cells. Greber, U.F., Willetts, M., Webster, P., Helenius, A. Cell (1993) [Pubmed]
  9. Three-dimensional structure of the HSV1 nucleocapsid. Schrag, J.D., Prasad, B.V., Rixon, F.J., Chiu, W. Cell (1989) [Pubmed]
  10. Correlation between structural transformation and cleavage of the major head protein of T4 bacteriophage. Laemmli, U.K., Amos, L.A., Klug, A. Cell (1976) [Pubmed]
  11. Structure of Sindbis virus core protein reveals a chymotrypsin-like serine proteinase and the organization of the virion. Choi, H.K., Tong, L., Minor, W., Dumas, P., Boege, U., Rossmann, M.G., Wengler, G. Nature (1991) [Pubmed]
  12. Structure of a major immunogenic site on foot-and-mouth disease virus. Logan, D., Abu-Ghazaleh, R., Blakemore, W., Curry, S., Jackson, T., King, A., Lea, S., Lewis, R., Newman, J., Parry, N. Nature (1993) [Pubmed]
  13. Three-dimensional structure of poliovirus at 2.9 A resolution. Hogle, J.M., Chow, M., Filman, D.J. Science (1985) [Pubmed]
  14. Intrinsic immunity: a front-line defense against viral attack. Bieniasz, P.D. Nat. Immunol. (2004) [Pubmed]
  15. Sequence of reovirus haemagglutinin predicts a coiled-coil structure. Bassel-Duby, R., Jayasuriya, A., Chatterjee, D., Sonenberg, N., Maizel, J.V., Fields, B.N. Nature (1985) [Pubmed]
  16. Human papillomavirus infections in nonmelanoma skin cancers from renal transplant recipients and nonimmunosuppressed patients. Shamanin, V., zur Hausen, H., Lavergne, D., Proby, C.M., Leigh, I.M., Neumann, C., Hamm, H., Goos, M., Haustein, U.F., Jung, E.G., Plewig, G., Wolff, H., de Villiers, E.M. J. Natl. Cancer Inst. (1996) [Pubmed]
  17. Sequence analysis of three Sindbis virus mutants temperature-sensitive in the capsid protein autoprotease. Hahn, C.S., Strauss, E.G., Strauss, J.H. Proc. Natl. Acad. Sci. U.S.A. (1985) [Pubmed]
  18. Localization of a poliovirus type 1 neutralization epitope in viral capsid polypeptide VP1. van der Werf, S., Wychowski, C., Bruneau, P., Blondel, B., Crainic, R., Horodniceanu, F., Girard, M. Proc. Natl. Acad. Sci. U.S.A. (1983) [Pubmed]
  19. Origin of JC polyomavirus variants associated with progressive multifocal leukoencephalopathy. Iida, T., Kitamura, T., Guo, J., Taguchi, F., Aso, Y., Nagashima, K., Yogo, Y. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  20. The role of the adenovirus protease on virus entry into cells. Greber, U.F., Webster, P., Weber, J., Helenius, A. EMBO J. (1996) [Pubmed]
  21. A domain of SV40 capsid polypeptide VP1 that specifies migration into the cell nucleus. Wychowski, C., Benichou, D., Girard, M. EMBO J. (1986) [Pubmed]
  22. Processing of the rough endoplasmic reticulum membrane glycoproteins of rotavirus SA11. Kabcenell, A.K., Atkinson, P.H. J. Cell Biol. (1985) [Pubmed]
  23. Acyclovir inhibition of Epstein-Barr virus replication. Datta, A.K., Colby, B.M., Shaw, J.E., Pagano, J.S. Proc. Natl. Acad. Sci. U.S.A. (1980) [Pubmed]
  24. Specific recognition and accelerated uncoating of retroviral capsids by the TRIM5alpha restriction factor. Stremlau, M., Perron, M., Lee, M., Li, Y., Song, B., Javanbakht, H., Diaz-Griffero, F., Anderson, D.J., Sundquist, W.I., Sodroski, J. Proc. Natl. Acad. Sci. U.S.A. (2006) [Pubmed]
  25. Positional cloning of the mouse retrovirus restriction gene Fv1. Best, S., Le Tissier, P., Towers, G., Stoye, J.P. Nature (1996) [Pubmed]
  26. Regulation of a new bacteriophage T4 gene, 69, that spans an origin of DNA replication. Macdonald, P.M., Mosig, G. EMBO J. (1984) [Pubmed]
  27. Trim5alpha protein restricts both HIV-1 and murine leukemia virus. Yap, M.W., Nisole, S., Lynch, C., Stoye, J.P. Proc. Natl. Acad. Sci. U.S.A. (2004) [Pubmed]
  28. Induction of chromosomal instability in colonic cells by the human polyomavirus JC virus. Ricciardiello, L., Baglioni, M., Giovannini, C., Pariali, M., Cenacchi, G., Ripalti, A., Landini, M.P., Sawa, H., Nagashima, K., Frisque, R.J., Goel, A., Boland, C.R., Tognon, M., Roda, E., Bazzoli, F. Cancer Res. (2003) [Pubmed]
  29. Crystal structure of the tricorn protease reveals a protein disassembly line. Brandstetter, H., Kim, J.S., Groll, M., Huber, R. Nature (2001) [Pubmed]
  30. A nucleoprotein complex mediates the integration of retroviral DNA. Bowerman, B., Brown, P.O., Bishop, J.M., Varmus, H.E. Genes Dev. (1989) [Pubmed]
  31. Unique region of the minor capsid protein of human parvovirus B19 is exposed on the virion surface. Rosenfeld, S.J., Yoshimoto, K., Kajigaya, S., Anderson, S., Young, N.S., Field, A., Warrener, P., Bansal, G., Collett, M.S. J. Clin. Invest. (1992) [Pubmed]
  32. Differential effect of phosphonoacetic acid on the expression of Epstein-Barr viral antigens and virus production. Nyormoi, O., Thorley-Lawson, D.A., Elkington, J., Strominger, J.L. Proc. Natl. Acad. Sci. U.S.A. (1976) [Pubmed]
  33. Cryo-electron microscopy studies of empty capsids of human parvovirus B19 complexed with its cellular receptor. Chipman, P.R., Agbandje-McKenna, M., Kajigaya, S., Brown, K.E., Young, N.S., Baker, T.S., Rossmann, M.G. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
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