FIGURE 4.
a, a plot of the significant shifts (Δδ ≥0. 4 ppm) observed for the major coat protein in Pf1 phage. The residues are colored on a yellow-green scale (see color bar), and the surfaces of the residues exhibiting shifts ≥0.4 ppm are shown explicitly. The strongest and majority of shifts are located in the hydrophobic C-terminal region. The sequence of the 46-amino acid coat protein is shown below the monomer, and residues with significant shifts are indicated on the subunit (gray color marks unassigned atoms). The model was generated with the program PyMOL using the coordinates of the Pf1L model 4IFM. b, chemical shift perturbation surface of subunits 0, +6, and +11 from the same model. b1, view from the interior of the virion at the three subunits. Subunit 0 is indicated by a white-to-red color scale (0–2 ppm) according to the observed absolute shift perturbation Δδ, and a surface is plotted for atoms with Δδ ≥0.4 ppm. Subunits +6 and +11 are indicated by a white-blue and white-green color scales, respectively. The gray color indicates unassigned residues. b2, view in b1 zoomed into the main perturbation region showing the intersubunit patches involving residues Gln0-16, Ala6-29, Ile6-32, Val11-35, Leu11-38, and Ile11-39 at the bottom (superscripts indicate subunit) and residues Ile0-12 and Ile6-26 just above. b3, 180° rotation of the view in b2, showing the same region from the outside of the virion. c, axial and side views of a 60 subunit portion (∼0.8%) of the capsid of Pf1 showing locations of observed chemical shift perturbations Δδ colored according to their absolute values in ppm (Fig. 2). For Δδ ≥0.4 ppm, van der Waals surfaces are shown; otherwise stick models without surfaces are used in c1–c3. c1, axial view is from the N-terminal ends of the subunits on the outside toward their C-terminal ends near the center. c2, axial view is from the opposite direction as in c1. In the side view of c3, surfaces are only for Δδ values ≥0.4, and in c4, surfaces are for all residues regardless of the shift perturbation. The gray colors indicate unassigned atoms including all non-carbon atoms but not hydrogens.