Fig. 6. Modeling a peptide structure into linker-associated densities visualized by cryo-EM difference imaging. Residues 103–110 of cellobiose dehydrogenase (Hallberg et al., 2000) are almost completely identical to the linker sequences (A). In (B), this peptide is shown (white α-carbon trace) docked into the difference density (pink mesh) from the T = 4 capsids. Quasi-equivalent core domain subunits are shown in green, yellow, red and blue. Five-fold (at left) and 2-fold (at right) symmetry axes are marked. In (C), the view is from the inside of the capsid. We propose that a semi-flexible hinge allows the linker to pivot, so that it serves as a spacer that prevents the protamine domains from intruding too closely into inter-core domain contacts, and also confers mobility on the protamine domains’ interactions with nucleic acid.