Figure 3. The clam-shaped nucleocapsid is important for the function of the viral genome.

(A) Loop pairs from the vertically adjacent N form the self-capping interface in the clam-shaped structure. Five loop pairs furthest from the seam are shown. Colors are as in Figure 1. (B) View of one loop pair of the clam-shaped structure. Seven residues (114–120) in the upper loop are labeled and the lower loop is docked into the EM density. (C) Raw micrograph of a single-headed helix from the N_Loop and the 2D classification of the filament tip (circled). Zoomed-in view of selected raw filaments (examples in dashed boxes) with two typical 2D classes on the tip shown. (D) N_WT was able to form double-headed filaments and functioned well in the minigenome assay. The retention volume of N_WT in gel filtration chromatography was ~47 ml (left) and the negative-stain image of this fraction consisted of a clam-shaped structure and filaments was zoomed in (middle). N_WT exhibited strong fluorescence signals in a minigenome assay in BSR-T7/5 cells (right). (E) The N_Loop formed filaments but was not functional in a minigenome assay. The retention volume of the N_Loop was ~47 ml, close to N_WT (left). Negative-stain EM showed more filaments than N_WT (middle). However, there was no fluorescence signal in the minigenome assay (right).

Figure 3—figure supplement 1. The summary and comparison of N and the derived mutants in the nucleocapsid assembly and their function in a minigenome assay.

Six N proteins including N_WT, N_{∆C-arm∆C-tail}, N_∆C-tail, N_{∆N-arm∆C-arm∆C-tail}, N_∆N-arm and N_Loop were subjected to gel filtration chromatography (left), negative stain EM (middle) and minigenome analyses (right). The negative stain image of N_WT was cropped from Figure 1—figure supplement 1B for convenient comparation.