Supplementary Figure Legends
Supplementary Figure 1 The Raman spectrum from crystals of PRD1. Raman
skeletal optical modes (SOM) result from (C-C) stretching vibrations of the lipid acyl
chains in the viral membrane. The Raman intensity profile of the SOM is diagnostic of
the distribution of unsaturated acyl side-chains between trans (strong bands at 1063 and
1125 cm-1) and gauche (strong band at 1082 cm-1, weaker bands at 1063 and 1125 cm-1)
rotamers, and therefore constitutes an indicator of gel and liquid crystalline phases in
lipid bilayers1. The PRD1 spectrum exhibits a Raman SOM profile (weak 1063 cm-1
band, relatively stronger 1082 cm-1 band) that corresponds closely with that obtained
previously on a solution of PRD1 in which the viral membrane was established to exist in
the liquid crystalline state2.
Supplementary Figure 2 Lateral correlation in electron density as a function of
icosahedral radius. Calculations were performed using the same surfaces as used to
generate Fig. 2a. The average electron density is shown in green with the layers of DNA
numbered and the inner (IL) and outer (OL) leaflets of the membrane marked. The red
line represents the correlation coefficient between the electron density for cell 1 and cell
2, calculated as a function of radius, after subtraction of the mean electron density for that
radius. The blue line represents the same calculation performed on cell 1 and cell 2 maps
which had been subjected to a smoothing regime. After convergence of the real space
phase refinement, the maps were averaged for a further five cycles, during which the
membrane and DNA regions were convolved with a Gaussian smearing function
(=0.8Å) on the second and fourth cycles. Note the increase in lateral correlation
suggesting that some of the high resolution features in the initial maps were spurious. The
smoothing regime used in Fig. 1d was similar except that the smearing of the membrane
and DNA regions was performed in two successive averaging cycles after convergence of
the phase refinement. The procedure used for the map displayed in Fig. 1a was more
conservative, the DNA and membrane regions being smoothed by repeated application of
the Gaussian smearing on successive averaging cycles, to convergence.
Supplementary Figure 3 Autocorrelation function for headgroup features in the outer
leaflet headgroup region of the membrane. The blue line is derived from the phosphate
group positions from a model membrane (a DMPC lipid bilayer supplied by Prof. Mark
Sansom, Laboratory of Molecular Biophysics, University of Oxford, UK). The red line is
derived from pseudo atoms placed into the electron density bumps in the headgroup
region of the outer leaflet (as seen in Fig. 1d).
Supplementary Figure 4 The lipid composition of the viral membrane. a, Atomic
structures of phosphatidyl glycerol (PG) and phosphatidyl ethanolamine (PE), the
principal lipid components of the viral membrane, with their main structural components
highlighted in yellow (fatty acid chains), purple (glycerol backbone), red (phosphate
group), green (glycerol headgroup) and blue (ethanolamine headgroup). At pH 7.2, the
phosphate group carries a single negative charge, and the ethanolamine a single positive
charge, so that PG is negatively charged and PE is zwitterionic. b, The phospholipid
headgroup composition of the viral membrane. c, A summary of the fatty acid
composition for PE (red bars) and non-PE (PG and CL, purple bars) type molecules,
plotted against the left y-axis. The x-axis gives the total number of fatty acid carbon
atoms per molecule and number of unsaturated double bonds. The corresponding number
of electrons per molecule for PE (red line, squares) and non-PE (purple, triangles)
headgroups is plotted against the right y-axis.
References
1.
Levin, I. W. in Advances in infrared and raman spectroscopy (ed. Clark, R. H. J.
H., R. E.) 1-48 (Wiley, Heyden, 1984).
2.
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, 102-15 (1996).