(A) An atomic model of an NWT double-headed filament from different views shows reciprocal capping between two single-headed spirals. Colors as in Figure 1. One single-headed spiral is highlighted by the black line and labeled ‘capping’. (B) An atomic model of an NLoop single-headed filament from different views with no cap and with the 5′ end of its RNA exposed. The supposed capping spiral, marked by the dashed line, is missing from the single-headed filament. (C) SDS-PAGE gels of NWT and NLoop after elastase digestion. There was a ~40-kDa main band with some smears in the elastase-digested NWT assay (left), while elastase cut the NLoop to form a ~30-kDa band (right). (D) Mass spectrum results identified peptides drawn on the atomic structure of N, indicating one additional cutting site on NLoop (gold scissors). The common regions mapped by Mass Spectrum in NWT and NLoop are colored in blue, and the unique region checked in NWT is shown in red. Five peptides were identified from the 40-kDa band of NWT and marked on the N atomic structure, leaving the CTD loops as the cutting site. Only four peptides were identified from the 30-kDa band of NLoop and marked on N atomic structure. Given the reduced molecular weight and the missing NTD peptide, another cutting site should exist within NTD. (E) Comparison of RNase A digesting NWT and NLoop at different timepoints. Both the clam-shaped structures and the filaments are counted. The numbers of oligomers in NWT and NLoop at 0 s are normalized to 100%. At 180 s, almost 100% disassembly of nucleocapsid was seen in NLoop whereas over 25% of filaments remained in NWT. (F) A cartoon depicts the hypothetical full protection provided to the viral RNA genome by NWT via the self-capping clam-shaped structure. When the clam-shaped structure is broken, nuclease is able to access the RNA 5’ end and can digest the whole RNA strand.