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The molecular organization of cypovirus polyhedra


Cypoviruses and baculoviruses are notoriously difficult to eradicate because the virus particles are embedded in micrometre-sized protein crystals called polyhedra1,2. The remarkable stability of polyhedra means that, like bacterial spores, these insect viruses remain infectious for years in soil. The environmental persistence of polyhedra is the cause of significant losses in silkworm cocoon harvests but has also been exploited against pests in biological alternatives to chemical insecticides3,4. Although polyhedra have been extensively characterized since the early 1900s5, their atomic organization remains elusive6. Here we describe the 2 Å crystal structure of both recombinant and infectious silkworm cypovirus polyhedra determined using crystals 5–12 micrometres in diameter purified from insect cells. These are the smallest crystals yet used for de novo X-ray protein structure determination7. We found that polyhedra are made of trimers of the viral polyhedrin protein and contain nucleotides. Although the shape of these building blocks is reminiscent of some capsid trimers, polyhedrin has a new fold and has evolved to assemble in vivo into three-dimensional cubic crystals rather than icosahedral shells. The polyhedrin trimers are extensively cross-linked in polyhedra by non-covalent interactions and pack with an exquisite molecular complementarity similar to that of antigen–antibody complexes. The resulting ultrastable and sealed crystals shield the virus particles from environmental damage. The structure suggests that polyhedra can serve as the basis for the development of robust and versatile nanoparticles for biotechnological applications8 such as microarrays9 and biopesticides4.

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Figure 1: Compact trimers are the building blocks of polyhedra.
Figure 2: Polyhedra are built around a tight scaffold of H1 helices.
Figure 3: Polyhedra are dense and sealed microcrystals containing nucleotides.
Figure 4: Proposed mechanism for the release of virus particles.


  1. Belloncik, S. & Mori, H. in The Insect Viruses (eds Miller, L. K. & Ball, L. A.) 337–369 (Plenum, New York, 1998)

    Book  Google Scholar 

  2. Miller, L. K. The Baculoviruses (Plenum, New York, 1997)

    Book  Google Scholar 

  3. Summers, M. D. Milestones leading to the genetic engineering of baculoviruses as expression vector systems and viral pesticides. In Advances in Virus Research (eds Bonning, B. C., Maramorosch, K. & Shatkin, A. J.), Ch. 68 3–73 (Academic Press, New York, 2006)

    Google Scholar 

  4. Chang, J. H. et al. An improved baculovirus insecticide producing occlusion bodies that contain Bacillus thuringiensis insect toxin. J. Invertebr. Pathol. 84, 30–37 (2003)

    Article  CAS  PubMed  Google Scholar 

  5. Glaser, R. W. & Chapman, J. W. The nature of the polyhedral bodies found in insect cells. Biol. Bull. 30, 367–390 (1916)

    Article  CAS  Google Scholar 

  6. Rohrmann, G. F. Polyhedrin structure. J. Gen. Virol. 67, 1499–1513 (1986)

    Article  CAS  PubMed  Google Scholar 

  7. Riekel, C., Burghammer, M. & Schertler, G. Protein crystallography microdiffraction. Curr. Opin. Struct. Biol. 15, 556–562 (2005)

    Article  CAS  PubMed  Google Scholar 

  8. Douglas, T. & Young, M. Viruses: making friends with old foes. Science 312, 873–875 (2006)

    Article  ADS  CAS  PubMed  Google Scholar 

  9. Ikeda, K. et al. Immobilization of diverse foreign proteins in viral polyhedra and potential application for protein microarrays. Proteomics 6, 54–66 (2006)

    Article  CAS  PubMed  Google Scholar 

  10. Fields, B. N., Knipe, D. M., Howley, P. M. & Griffin, D. E. Field's Virology (Lippincott Williams & Wilkins, Philadelphia, 2001)

    Google Scholar 

  11. Zhang, H. et al. Visualization of protein-RNA interactions in cytoplasmic polyhedrosis virus. J. Virol. 73, 1624–1629 (1999)

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Hill, C. L. et al. The structure of a cypovirus and the functional organization of dsRNA viruses. Nature Struct. Mol. Biol. 6, 565–568 (1999)

    Article  CAS  Google Scholar 

  13. Thorne, R. E., Stum, Z., Kmetko, J., O'Neill, K. & Gillilan, R. Microfabricated mounts for high-throughput macromolecular cryocrystallography. J. Appl. Cryst. 36, 1455–1460 (2003)

    Article  CAS  Google Scholar 

  14. Doye, J. P. K. & Poon, W. C. K. Protein crystallization in vivo. Curr. Opin. Colloid Interf. Sci. 11, 40–46 (2006)

    Article  CAS  Google Scholar 

  15. Grimes, J., Basak, A. K., Roy, P. & Stuart, D. The crystal structure of bluetongue virus VP7. Nature 373, 167–170 (1995)

    Article  ADS  CAS  PubMed  Google Scholar 

  16. Liemann, S., Chandran, K., Baker, T. S., Nibert, M. L. & Harrison, S. C. Structure of the reovirus membrane-penetration protein, Mu1, in a complex with its protector protein, Sigma3. Cell 108, 283–295 (2002)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Coulibaly, F. et al. The birnavirus crystal structure reveals structural relationships among icosahedral viruses. Cell 120, 761–772 (2005)

    Article  CAS  PubMed  Google Scholar 

  18. Wodak, S. J. & Janin, J. Structural basis of macromolecular recognition. Adv. Protein Chem. 61, 9–73 (2002)

    Article  PubMed  Google Scholar 

  19. Lawrence, M. C. & Colman, P. M. Shape complementarity at protein/protein interfaces. J. Mol. Biol. 234, 946–950 (1993)

    Article  CAS  PubMed  Google Scholar 

  20. Fujiwara, T. et al. Xray diffraction studies of the polyhedral inclusion bodies of nuclear and cytoplasmic polyhedrosis viruses. Appl. Entomol. Zool. Jpn 19, 402–403 (1984)

    Article  Google Scholar 

  21. Anduleit, K. et al. Crystal lattice as biological phenotype for insect viruses. Protein Sci. 14, 2741–2743 (2005)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Mori, H. et al. Expression of Bombyx mori cytoplasmic polyhedrosis virus polyhedrin in insect cells by using a baculovirus expression vector, and its assembly into polyhedra. J. Gen. Virol. 74, 99–102 (1993)

    Article  CAS  PubMed  Google Scholar 

  23. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. In Methods in Enzymology (eds Carter, C. W. & Sweet, R. M.) Ch. 276 307–326 (Academic Press, New York, 1997)

    Google Scholar 

  24. Schneider, T. R. & Sheldrick, G. M. Substructure solution with SHELXD. Acta Crystallogr. D 58, 1772–1779 (2002)

    Article  PubMed  Google Scholar 

  25. de La Fortelle, E. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. In Methods in Enzymology (eds Carter, C. W. & Sweet, R. M.) Ch. 276 472–494 (Academic Press, New York, 1997)

    Google Scholar 

  26. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997)

    Article  CAS  PubMed  Google Scholar 

  27. Lovell, S. C. et al. Structure validation by Cα geometry: φ, ψ and Cβ deviation. Proteins 50, 437–450 (2003)

    Article  CAS  PubMed  Google Scholar 

  28. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  29. Krissinel, E. & Henrick, K. Detection of protein-assemblies in crystals. In Lecture Notes in Computer Science (ed. Berthold, M. R.) Ch. 3695 163–174 (Springer, Berlin/Heidelberg, 2005)

    Google Scholar 

  30. Kleywegt, G. J. & Jones, T. A. Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr. D 50, 178–185 (1994)

    Article  CAS  PubMed  Google Scholar 

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We are very grateful for support from E. N. Baker. We thank R. E. Thorne for providing MicroMesh mounts; J. Taylor, A. Mitra and colleagues at SBS for critically reading the manuscript; and M. Middleditch, C. Hobbis, R. Graves, R. Bunker, A. Wagner, E. Pohl and J. Diez for experimental help. S.G. is funded by the Swiss NCCR Structural Biology and E.C. by a TEAC Bright Futures doctoral scholarship. This work was supported by the NZ FRST (F.C.), the UARC (P.M.), the Maurice Wilkins Centre for Molecular Biodiscovery (E.C.) and grants for Regional Consortium Research Development Work from the Kansai Bureau of METI (K.I. and H.M.), from CREST by JST (H.M.) and a JSPS Invitation Fellowship for Research in Japan (P.M.).

Structures of polyhedrins from infectious, recombinant and kinase-containing polyhedra have been deposited in the Protein Data Bank with accession codes 2OH5, 2OH6 and 2OH7.

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Correspondence to Peter Metcalf.

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Coulibaly, F., Chiu, E., Ikeda, K. et al. The molecular organization of cypovirus polyhedra. Nature 446, 97–101 (2007).

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