Skip to main content

Use of Non-Crystallographic Symmetry for Ab Initio Phasing of Virus Structures

  • Chapter
Direct Methods for Solving Macromolecular Structures

Part of the book series: NATO ASI Series ((ASIC,volume 507))

Abstract

Several virus structures have now been determined through ab initio phasing at very low (~20A) resolution followed by extension to high resolution using their non-crystallographic symmetry (NCS). The methods are described, and post-mortem investigations of phase determination are analyzed, particularly for relevance to the more challenging general case of ab initio determination of protein structure.

To whom crrespondence should be addressed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Acknowledgments & References

  1. The structure determinations were supported by the National Institutes of Health (MGR; JEJ), the National Science Foundation (MGR) and the Lucille P. Markey Charitable Trust (MGR). Recent work was supported by the National Science Foundation (MSC).

    Google Scholar 

  2. Rossmann, M. G. (1995) Ab initio phase determination and phase extension using non-crystallographic symmetry, Current Opinion in Structural Biology 5, 650–655

    Article  Google Scholar 

  3. Chapman, M. S., Blanc, E., McKenna, R., Munshi, S., Rossmann, M. G. and Tsao, J. (1997) Use of non-crystallographic symmetry for ab initio phasing of virus structures, in Fortier, S. (ed.), NATO Advanced Study Institute on Direct Methods for Solving Macromolecular Structures, Kluwer Academic Publishers, Dordrecht, The Netherlands

    Google Scholar 

  4. Chapman, M. S. (1997) Introduction to the use of non-crystallographic symmetry in phasing, in Fortier, S. (ed.), NATO Advanced Study Institute on Direct Methods for Solving Macromolecular Structures, Kluwer Academic Publishers, Dordrecht, The Netherlands

    Google Scholar 

  5. Arnold, E. and Rossmann, M. G. (1986) Effect of errors, redundancy, and solvent content in the molecular replacement procedure for the structure determination of biological macromolecules, Proc. Natl. Acad. Sci. USA 83, 5489–93

    Article  ADS  Google Scholar 

  6. Chapman, M. S., Tsao, J. and Rossmann, M. G. (1992) Ab initio Phase Determination for Spherical Viruses: Parameter Determination for Spherical Shell Models, Acta Crystallographica A48, 301–312

    Google Scholar 

  7. Caspar, D. L. D. and Klug, A. (1962) Physical principles in the constructuion of regular viruses, Cold Spring Harbor Symposium in Quantitative Biology 27, 1–24

    Article  Google Scholar 

  8. Tong, L. and Rossmann, M. G. (1990) The Locked Rotation Function, Acta Crystallographica A46, 783–792

    Google Scholar 

  9. Tong, L. (1996) The Locked Translation Function and Other Applications of a Patterson Correlation Function, Acta Crystallographica A52, 476–79

    Google Scholar 

  10. Tsao, J., Chapman, M. S., Wu, H., Agbandje, M., Keller, W. and Rossmann, M. G. (1992) Structure Determination of Monoclinic Canine Parvovirus, Acta Crystallographica B48, 75–88

    Google Scholar 

  11. Burling, F. T., Weis, W. I., Flaherty, K. M. and Briinger, A. (1996) Direct Observation of Protein Solvation and Discrete Disorder Using Experimental Crystallographic Phases, Science 271, 72–77

    Article  ADS  Google Scholar 

  12. Zhou, G., Wang, J., Blanc, E. and Chapman, M. S. (1997) Determination of the Relative Precision of Atoms in a Macromolecular Structure, Acta Crystallographica submitted

    Google Scholar 

  13. Johnson, J. E., Akimoto, T., Suck, D., Rayment, I. and Rossmann, M. G. (1976) The Structure of Southern Bean Mosaic Virus at 22.5 00C4; Resolution, Virology 75, 394–400

    Article  Google Scholar 

  14. Rayment, I., Baker, T. S., Caspar, D. L. D. and Murakami, W. T. (1982) Polyoma virus capsid structure at 22.5 à resoution, Nature 295, 110–15

    Article  ADS  Google Scholar 

  15. Stehl, T., Yan, Y. and Harrison, S. C. (1994) The structure of murine Polyomavirus complexed with an oligosaccharide receptor fragment, Nature 369, 160–3

    Article  ADS  Google Scholar 

  16. Lunin, V. Y., Lunina, N. L., Petrova, T. E., Vernoslova, E. A., Urzhumtsev, D. A. G. and Podjarny, A. (1995) On the ab initio solution of the phase problem for macromolecules at very low resolution: the few atoms model method, Acta Crystallographica D51, 896–903

    Google Scholar 

  17. Podjarny, A. (1997) Model based approaches at very low resolution, in Fortier, S. (ed.), NATO Advanced Study Institute on Direct Methods for Solving Macromolecular Structures, Kluwer Academic Publishers, Dordrecht, The Netherlands

    Google Scholar 

  18. Subiah, S. (1991) Low-resolution Real-Space Envelopes: An Approach to the Ab Initio Macromolecular Phase Problem, Science 252, 128–133

    Article  ADS  Google Scholar 

  19. Miller, S. T., Hogle, J. M. and Filman, D. J. (1996) A Genetic Algorithm for the Ab Initio Phasing of Icosahedral Viruses, Acta Crystallographica D52, 235–251

    Google Scholar 

  20. Tsao, J., Chapman, M. S. and Rossmann, M. G. (1992) Ab initio Phase Determination for Viruses with High Symmetry: A Feasibility Study, Acta Crystallographica A48, 293–301

    Google Scholar 

  21. McKenna, R., Xia, D., Willingmann, P., Hag, L. and Rossmann, M. G. (1992) Structure Determination of Bacteriophage (|)X174, Acta Cryst. B48, 499–511

    Google Scholar 

  22. Toyoshima, C. and Unwin, N. (1988) Contrast transfer of frozen hydrated specimins: Determination from pairs of defocussed images, Ultramicroscopy 25, 279–92

    Article  Google Scholar 

  23. Munshi, S., Liljas, L., Cavarelli, J., Bomu, W., McKinney, B., Reddy, V. and Johnson, J. E. (1996) The 2.8 Åstructure of a T=4 animal virus and its implications for membrane translocation of RNA, Journal of Molecular Biology 261, 1–10

    Article  Google Scholar 

  24. Munshi, S., Liljas, L. and Johnson, J. E. (1997) Joys and Traps of Phase Extension: Structure Determination of Nudaurelia capensis O) Virus, Acta Crystallographica in preparation

    Google Scholar 

  25. Rossmann, M. G., Arnold, E., Erickson, J. W., Frankenberger, E. A., Griffith, J. P., Hecht, H., Johnson, J. E., Kamer, G., Luo, M., Mosser, A., Rueckert, R., Sherry, B. and Vriend, G. (1985) Structure of human common cold virus and functional relationship to other picornaviruses, Nature 317, 145–153

    Article  ADS  Google Scholar 

  26. Rossmann, M. G., McKenna, R., Tong, L., Xia, D., Dai, J.-B., Wu, H., Choi, H.-K. and Lynch, R. E. (1992) Molecular Replacement Real-Space Averaging, J. Appl. Cryst. 25, 166–80

    Article  Google Scholar 

  27. Wang, B. C. (1985) Resolution of the Phase Ambiguity in Macromolecular Crystallography, Methods in Enzymology 115, 90–112

    Article  Google Scholar 

  28. Chapman, M. S., Minor, I., Rossmann, M. G., Diana, G. D. and Andries, K. (1991) Human rhinovirus 14 complexed with antiviral compound R 61837, Journal of Molecular Biology 217, 455–63

    Article  Google Scholar 

  29. Jones, T. A. (1992) a, yaap, asap, @£? A set of averaging programs, in Dodson, E., Gover, S. and Wolf, W. (ed.), Proceedings of the CCP4 Study Weekend, Science and Engineering Research Council, pp. 91–105

    Google Scholar 

  30. Cornea-Hasegan, M. A., Zhang, Z., Lynch, R. E., Marinescu, D. C., Hadfield, A., Muckelbauer, J. K., Munshi, S. and Rossmann, M. G. (1996) Phase refinement and extension by means of non-cry stallographic symmetry averaging using parallel computers, Acta Crystallographica D51, 749–59

    Google Scholar 

  31. Valegard, K., Liljas, L., Fridborg, K. and Unge, T. (1991) Structure Determination of the Bacteriophage MS2, Acta Crystallographica B47, 949–960

    Google Scholar 

  32. Acharya, R., Fry, E., Stuart, D., Fox, G., Rowlands, D. and Brown, F. (1989) The three-dimensional structure of foot-and-mouth disease virus at 2.9 A resolution, Nature 337, 709–716

    Article  ADS  Google Scholar 

  33. Larson, S. B., Koszelak, S., Day, J., Greenwood, A., Dodds, J. A. and McPherson, A. (1993) Three-dimensional Structure of Satellite Tobacco Mosaic Virus at 2.9 Åresoluion., Journal of Molecular Biology 231, 375–91

    Article  Google Scholar 

  34. Ban, N. and McPherson, A. (1995) The structure of satellite panicum mosaic virus at 1.9 A resolution, Nature Structural Biology 2, 882–890

    Article  Google Scholar 

  35. Kim, S., Smith, T. J., Chapman, M. S., Rossmann, M. G., Pevear, D. C., Dutko, F. J., Felock, P. J., Diana, G. D. and McKinlay, M. A. (1989) Crystal Structure of Human Rhinovirus Serotype 1A (HRV1A), J. Mol. Biol. 210, 91–111

    Article  Google Scholar 

  36. Chapman, M. S. (1995) Restrained Real-Space Macromolecular Atomic Refinement using a New Resolution-Dependent Electron Density Function, Acta Crystallographica A51, 69–80

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1998 Springer Science+Business Media New York

About this chapter

Cite this chapter

Chapman, M.S. et al. (1998). Use of Non-Crystallographic Symmetry for Ab Initio Phasing of Virus Structures. In: Fortier, S. (eds) Direct Methods for Solving Macromolecular Structures. NATO ASI Series, vol 507. Springer, Dordrecht. https://doi.org/10.1007/978-94-015-9093-8_38

Download citation

  • DOI: https://doi.org/10.1007/978-94-015-9093-8_38

  • Publisher Name: Springer, Dordrecht

  • Print ISBN: 978-90-481-4994-0

  • Online ISBN: 978-94-015-9093-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics