Structure of a viral procapsid with molecular scaffolding

Abstract

The assembly of a macromolecular structure proceeds along an ordered morphogenetic pathway, and is accomplished by the switching of proteins between discrete conformations as they are added to the nascent assembly1,2,3. Scaffolding proteins often play a catalytic role in the assembly process1,2,4, rather like molecular chaperones5. Although macromolecular assembly processes are fundamental to all biological systems, they have been characterized most thoroughly in viral systems, such as the icosahedral Escherichia coli bacteriophage φX174 (refs 6, 7). The φX174 virion contains the proteins F, G, H and J7,8. During assembly, two scaffolding proteins B and D are required for the formation of a 108S, 360-Å-diameter procapsid from pentameric precursors containing the F, G and H proteins6,9. The procapsid contains 240 copies of protein D, forming an external scaffold, and 60 copies each of the internal scaffolding protein B, the capsid protein F, and the spike protein G9,10. Maturation involves packaging of DNA and J proteins and loss of protein B, producing a 132S intermediate6,7. Subsequent removal of the external scaffold yields the mature virion. Both the F and G proteins have the eight-stranded antiparallel β-sandwich motif8,11 common to many plant and animal viruses12,13. Here we describe the structure of a procapsid-like particle at 3.5-Å resolution, showing how the scaffolding proteins coordinate assembly of the virus by interactions with the F and G proteins, and showing that the F protein undergoes conformational changes during capsid maturation.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Isosurface representation of a 10-Å resolution electron-density map of the whole closed procapsid particle, viewed down a 2-fold axis.
Figure 2: Cα backbone plot of the F protein in the closed procapsid (red).
Figure 3: Ribbon diagram29 showing the arrangement of the four D scaffolding proteins in one icosahedral asymmetric unit triangle, coloured as in Fig. 1a, viewed down a 2-fold axis.
Figure 4: Structural comparison of the D subunits.
Figure 5: Early steps in the assembly pathway of φX174.

References

  1. 1

    King, J. in Biological Regulation and Development Vol. 2, Molecular Organization and Cell Function(ed. Goldberger, R. F.) 101–132 (Plenum, New York, (1980).

    Google Scholar 

  2. 2

    Casjens, S. & Hendrix, R. in The Bacteriophages Vol. 1(ed. Calendar, R.) 15–75 (Plenum, New York, (1988).

    Google Scholar 

  3. 3

    Oosawa, F. & Asakura, S. Thermodynamics of the Polymerization of Proteins(Academic, London, (1975).

    Google Scholar 

  4. 4

    Preston, V. G., al-Kobaisi, M. F., McDougall, I. M. & Rixon, F. J. The herpes simplex virus gene UL26 proteinase in the presence of the UL26.5 gene product promotes the formation of scaffold-like structures. J. Gen. Virol. 75, 2355–2366 (1994).

    CAS  Article  Google Scholar 

  5. 5

    Martin, J. & Hartl, F. U. Chaperone-assisted protein folding. Curr. Opin. Struct. Biol. 7, 41–52 (1997).

    CAS  Article  Google Scholar 

  6. 6

    Hayashi, M. in The Single-Stranded DNA Phages(eds Denhardt, D. T., Dressler, D. & Ray, D. S.) 531–547 (Cold Spring Harbor Laboratory Press, NY, (1978).

    Google Scholar 

  7. 7

    Hayashi, M., Aoyama, A., Richardson, D. L. J & Hayashi, M. N. in The Bacteriophages Vol. 2(ed. Calendar, R.) 1–71 (Plenum, New York, (1988).

    Google Scholar 

  8. 8

    McKenna, R. et al. Atomic structure of single-stranded DNA bacteriophage φX174 and its functional implications. Nature 355, 137–143 (1992).

    ADS  CAS  Article  Google Scholar 

  9. 9

    Mukai, R., Hamatake, R. K. & Hayashi, M. Isolation and identification of bacteriophage φX174 prohead. Proc. Natl Acad. Sci. USA 76, 4877–4881 (1979).

    ADS  CAS  Article  Google Scholar 

  10. 10

    Ilag, L. L. et al. DNA packaging intermediates of bacteriophage φX174. Structure 3, 353–363 (1995).

    CAS  Article  Google Scholar 

  11. 11

    McKenna, R., Ilag, L. L. & Rossmann, M. G. Analysis of the single-stranded DNA bacteriophage φX174, refined at a resolution of 3.0 Å. J. Mol. Biol. 237, 517–543 (1994).

    CAS  Article  Google Scholar 

  12. 12

    Harrison, S. C., Skehel, J. J. & Wiley, D. C. in Fields Virology Vol. 1(eds Fields, B. N., Knipe, D. M. & Howley, P. M.) 59–99 (Lippincott-Raven, Philadelphia, (1996).

    Google Scholar 

  13. 13

    Rossmann, M. G. & Johnson, J. E. Icosahedral RNA virus structure. Annu. Rev. Biochem. 58, 533–573 (1989).

    CAS  Article  Google Scholar 

  14. 14

    Rossmann, M. G. The molecular replacement method. Acta Crystallogr. A 46, 73–82 (1990).

    Article  Google Scholar 

  15. 15

    Dokland, T. & Murialdo, H. Structural transitions during maturation of bacteriophage lambda capsids. J. Mol. Biol. 233, 682–694 (1993).

    CAS  Article  Google Scholar 

  16. 16

    Prasad, B. V. V. et al. Three-dimensional transformation of capsids associated with genome packaging in a bacterial virus. J. Mol. Biol. 231, 65–74 (1993).

    CAS  Article  Google Scholar 

  17. 17

    McKenna, R., Bowman, B. R., Ilag, L. L., Rossmann, M. G. & Fane, B. A. Atomic structure of the degraded procapsid particle of the bacteriophage G4: induced structural changes in the presence of calcium ions and functional implications. J. Mol. Biol. 256, 736–750 (1996).

    CAS  Article  Google Scholar 

  18. 18

    Caspar, D. L. D. & Klug, A. Physical principles in the construction of regular viruses. Cold Spring Harb. Symp. Quant. Biol. 27, 1–24 (1962).

    CAS  Article  Google Scholar 

  19. 19

    Farber, M. B. Purification and properties of bacteriophage φX174 gene D products. J. Virol. 17, 1027–1037 (1976).

    CAS  PubMed  PubMed Central  Google Scholar 

  20. 20

    Ekechukwu, M. C. & Fane, B. A. Characterization of the morphogenetic defects conferred by cold-sensitive prohead accessory and scaffolding proteins of φX174. J. Bacteriol. 177, 829–830 (1995).

    CAS  Article  Google Scholar 

  21. 21

    Fane, B. A., Shien, S. & Hayashi, M. Second-site suppressors of a cold sensitive external scaffolding protein of bacteriophage φX174. Genetics 134, 1003–1011 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22

    Ekechukwu, M. C., Oberste, D. J. & Fane, B. A. Host and φX174 mutations affecting the morphogenesis or stabilization of the 50S complex, a single-stranded DNA synthesizing intermediate. Genetics 140, 1167–1174 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23

    Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276A, 307–326 (1997).

    Article  Google Scholar 

  24. 24

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

    Article  Google Scholar 

  25. 25

    Tong, L. & Rossmann, M. G. The locked rotation function. Acta Crystallogr. A 46, 783–792 (1990).

    Article  Google Scholar 

  26. 26

    Rossmann, M. G. et al. Molecular replacement real-space averaging. J. Appl. Crystallogr. 25, 166–180 (1992).

    CAS  Article  Google Scholar 

  27. 27

    Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

  28. 28

    Rossmann, M. G. & Blow, D. M. The detection of sub-units within the crystallographic asymmetric unit. Acta Crystallogr. 15, 24–31 (1962).

    CAS  Article  Google Scholar 

  29. 29

    Kraulis, P. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

Download references

Acknowledgements

We thank the staff at the Cornell High Energy Synchrotron Source and the National Light Source staff at beam line X12 for providing the data collection facilities; W. F. Bean for help with computational work; and S. Wilder for help in the preparation of this manuscript. This study was supported by a National Science Foundation grant to M.G.R., an NIH grant to B.A.F., a Robert and Richard Rizzo Memorial Fund grant and an NIH grant to N.L.I., a Lucille P. Markey Foundation award to Purdue University, and a Purdue University reinvestment program grant. T.D. was supported by a European Molecular Biology Organization long-term postdoctoral fellowship for some of the time of this work.

Author information

Affiliations

Authors

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Dokland, T., McKenna, R., Ilag, L. et al. Structure of a viral procapsid with molecular scaffolding. Nature 389, 308–313 (1997). https://doi.org/10.1038/38537

Download citation

Further reading

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing