Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Membrane structure and interactions with protein and DNA in bacteriophage PRD1

Abstract

Membranes are essential for selectively controlling the passage of molecules in and out of cells and mediating the response of cells to their environment. Biological membranes and their associated proteins present considerable difficulties for structural analysis. Although enveloped viruses have been imaged at about 9 Å resolution by cryo-electron microscopy and image reconstruction1,2, no detailed crystallographic structure of a membrane system has been described. The structure of the bacteriophage PRD1 particle, determined by X-ray crystallography at about 4 Å resolution, allows the first detailed analysis of a membrane-containing virus3. The architecture of the viral capsid and its implications for virus assembly are presented in the accompanying paper3. Here we show that the electron density also reveals the icosahedral lipid bilayer, beneath the protein capsid, enveloping the viral DNA. The viral membrane contains about 26,000 lipid molecules asymmetrically distributed between the membrane leaflets. The inner leaflet is composed predominantly of zwitterionic phosphatidylethanolamine molecules, facilitating a very close interaction with the viral DNA, which we estimate to be packaged to a pressure of about 45 atm, factors that are likely to be important during membrane-mediated DNA translocation into the host cell. In contrast, the outer leaflet is enriched in phosphatidylglycerol and cardiolipin, which show a marked lateral segregation within the icosahedral asymmetric unit. In addition, the lipid headgroups show a surprising degree of order.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Membrane architecture.
Figure 2: Membrane–DNA interactions.

Similar content being viewed by others

References

  1. Zhang, W. et al. Visualization of membrane protein domains by cryo-electron microscopy of dengue virus. Nature Struct. Biol. 10, 907–912 (2003)

    Article  CAS  Google Scholar 

  2. Mancini, E. J., Clarke, M., Gowen, B. E., Rutten, T. & Fuller, S. D. Cryo-electron microscopy reveals the functional organization of an enveloped virus, Semliki Forest virus. Mol. Cell 5, 255–266 (2000)

    Article  CAS  Google Scholar 

  3. Abrescia, N. G. et al. Insights into assembly from structural analysis of bacteriophage PRD1. Nature doi:10.1038/nature03056 (this issue)

  4. Bamford, D. H., Caldentey, J. & Bamford, J. K. Bacteriophage PRD1: a broad host range dsDNA tectivirus with an internal membrane. Adv. Virus Res. 45, 281–319 (1995)

    Article  CAS  Google Scholar 

  5. Butcher, S. J., Bamford, D. H. & Fuller, S. D. DNA packaging orders the membrane of bacteriophage PRD1. EMBO J. 14, 6078–6086 (1995)

    Article  CAS  Google Scholar 

  6. San Martín, C. et al. Combined EM/X-ray imaging yields a quasi-atomic model of the adenovirus-related bacteriophage PRD1 and shows key capsid and membrane interactions. Structure 9, 917–930 (2001)

    Article  Google Scholar 

  7. Rydman, P. S., Bamford, J. K. & Bamford, D. H. A minor capsid protein P30 is essential for bacteriophage PRD1 capsid assembly. J. Mol. Biol. 313, 785–795 (2001)

    Article  CAS  Google Scholar 

  8. Rydman, P. S. et al. Bacteriophage PRD1 contains a labile receptor-binding structure at each vertex. J. Mol. Biol. 291, 575–587 (1999)

    Article  CAS  Google Scholar 

  9. Strömsten, N. J., Bamford, D. H. & Bamford, J. K. The unique vertex of bacterial virus PRD1 is connected to the viral internal membrane. J. Virol. 77, 6314–6321 (2003)

    Article  Google Scholar 

  10. Gowen, B., Bamford, J. K., Bamford, D. H. & Fuller, S. D. The tailless icosahedral membrane virus PRD1 localizes the proteins involved in genome packaging and injection at a unique vertex. J. Virol. 77, 7863–7871 (2003)

    Article  CAS  Google Scholar 

  11. Bamford, D. & Mindich, L. Structure of the lipid-containing bacteriophage PRD1: disruption of wild-type and nonsense mutant phage particles with guanidine hydrochloride. J. Virol. 44, 1031–1038 (1982)

    CAS  PubMed  PubMed Central  Google Scholar 

  12. Rydman, P. S. & Bamford, D. H. Bacteriophage PRD1 DNA entry uses a viral membrane-associated transglycosylase activity. Mol. Microbiol. 37, 356–363 (2000)

    Article  CAS  Google Scholar 

  13. Rydman, P. S. & Bamford, D. H. The lytic enzyme of bacteriophage PRD1 is associated with the viral membrane. J. Bacteriol. 184, 104–110 (2002)

    Article  CAS  Google Scholar 

  14. Bamford, J. K. et al. Diffraction quality crystals of PRD1, a 66-MDa dsDNA virus with an internal membrane. J. Struct. Biol. 139, 103–112 (2002)

    Article  CAS  Google Scholar 

  15. Grahn, A. M., Daugelavicius, R. & Bamford, D. H. Sequential model of phage PRD1 DNA delivery: active involvement of the viral membrane. Mol. Microbiol. 46, 1199–1209 (2002)

    Article  CAS  Google Scholar 

  16. Davis, T. N., Muller, E. D. & Cronan, J. E. Jr The virion of the lipid-containing bacteriophage PR4. Virology 120, 287–306 (1982)

    Article  CAS  Google Scholar 

  17. Grahn, A. M., Caldentey, J., Bamford, J. K. & Bamford, D. H. Stable packaging of phage PRD1 DNA requires adsorption protein P2, which binds to the IncP plasmid-encoded conjugative transfer complex. J. Bacteriol. 181, 6689–6696 (1999)

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Tuma, R., Bamford, J. K., Bamford, D. H. & Thomas, G. J. Jr Structure, interactions and dynamics of PRD1 virus. II. Organization of the viral membrane and DNA. J. Mol. Biol. 257, 102–115 (1996)

    Article  CAS  Google Scholar 

  19. Laurinavicius, S., Käkelä, R., Somerharju, P. & Bamford, D. H. Phospholipid molecular species profiles of tectiviruses infecting Gram-negative and Gram-positive hosts. Virology 322, 328–336 (2004)

    Article  CAS  Google Scholar 

  20. Nagle, J. F. & Tristram-Nagle, S. Structure of lipid bilayers. Biochim. Biophys. Acta 1469, 159–195 (2000)

    Article  CAS  Google Scholar 

  21. Struth, B. et al. Organization of two-dimensional phospholipid monolayers on a gel-forming substrate. Phys. Rev. Lett. 88, 025502 (2002)

    Article  ADS  Google Scholar 

  22. Cerritelli, M. E. et al. Encapsidated conformation of bacteriophage T7 DNA. Cell 91, 271–280 (1997)

    Article  CAS  Google Scholar 

  23. Livolant, F. & Leforestier, A. Condensed phases of DNA: Structures and phase transitions. Prog. Polym. Sci. 21, 1115–1164 (1996)

    Article  CAS  Google Scholar 

  24. Smith, D. E. et al. The bacteriophage φ29 portal motor can package DNA against a large internal force. Nature 413, 748–752 (2001)

    Article  ADS  CAS  Google Scholar 

  25. Evans, E., Heinrich, V., Ludwig, F. & Rawicz, W. Dynamic tension spectroscopy and strength of biomembranes. Biophys. J. 85, 2342–2350 (2003)

    Article  CAS  Google Scholar 

  26. Bevers, E. M., Comfurius, P., Dekkers, D. W. C. & Zwaal, R. F. A. Lipid translocation across the plasma membrane of mammalian cells. Biochim. Biophys. Acta 1439, 317–330 (1999)

    Article  CAS  Google Scholar 

  27. Casper, D. L. & Kirschner, D. A. Myelin membrane structure at 10 Å resolution. Nature New Biol. 231, 46–52 (1971)

    Article  Google Scholar 

  28. Brunger, A. T. X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR (Yale University Press, New Haven, Connecticut, 1992)

    Google Scholar 

  29. Tao, Y. et al. Assembly of a tailed bacterial virus and its genome release studied in three dimensions. Cell 95, 431–437 (1998)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank M. Sansom and P. Bond (Laboratory of Molecular Biophysics, University of Oxford) for providing coordinates of lipid bilayers, the staff at the European Synchrotron Radiation Facility for beamline support, and E. Mancini for assistance with data collection. This investigation was supported by a research grant from the Academy of Finland to J.K.H.B., research grants and the Finnish Centre of Excellence Program (2000–2005) from the Academy of Finland to D.H.B., the Biotechnology and Biological Sciences Research Council and the Medical Research Council, UK, and a grant from the Human Frontiers Science Program to D.H.B. and D.I.S. J.M.G. is supported by the Royal Society, and D.I.S. by the UK Medical Research Council.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Dennis H. Bamford or David I. Stuart.

Ethics declarations

Competing interests

The authors declare that they have no competing financial interests.

Supplementary information

Supplementary Methods

1. The acquisition of Raman spectra from crystals of PRD1; 2. Initial estimation of the bulk solvent electron density in cell 2 crystals; 3. Calculation of the mean number of electrons per lipid for the different headgroup species from the mass spectrometry data; 4. Calculation of the number of lipids in the viral membrane based on published data in lipid molecular volumes. (DOC 26 kb)

Supplementary Figure 1

The Raman spectrum from PRD1 crystals showing that the viral lipids are in the liquid crystalline phase. (JPG 18 kb)

Supplementary Figure 2

Analysis of the lateral order in the electron density for the membrane. (JPG 35 kb)

Supplementary Figure 3

Autocorrelation function for features in the membrane outer leaflet headgroups. (JPG 18 kb)

Supplementary Figure 4

Summary of the mass spectrometry data on the lipid composition of the viral membrane (JPG 35 kb)

Supplementary Figure Legends (DOC 31 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Cockburn, J., Abrescia, N., Grimes, J. et al. Membrane structure and interactions with protein and DNA in bacteriophage PRD1. Nature 432, 122–125 (2004). https://doi.org/10.1038/nature03053

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature03053

This article is cited by

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