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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.

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

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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.

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

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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)

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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

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