P3-induced abnormal aggregation on the full-length MERS-CoV N protein. (A–E) SAXS analysis of the full-length MERS-CoV N protein. (A) Normalized results from GNOM showing pairwise distance distribution P(r) and maximum distance. The radius of gyration fitted to 207 and 230 Å for the N protein and the N-P3 complex, respectively. “r” represents pairwise distances. (B, C) Scattering profiles of the N protein (B) and the N-P3 complex (C) and normalization fitting with GNOM (dashed lines). (D, E) Representative models of the N protein (D) and the N-P3 complex (E) generated by CRYSOL simulations of the SAXS data. Only α carbons are shown. NTD (yellow), CTD (green), and disorder region (cyan). (F, G) Conformation (F) and stability (G) analyses based on FL spectra of the MERS-CoV N protein (1 μM) incubated with P3 (10 μM) for 1 h in a buffer consisting of 50 mM Tris-HCl, 150 mM NaCl (pH 8.3). (H) Schematic of the P3 inhibition mechanism. Left panel: in the absence of RNA, N proteins organize as a dimeric building block contributed by N-CTD dimerization. Middle panel: P3 promoted the dimerization of N-NTDs from different building blocks, by which the distance between CTD cuboids was shortened and N protein aggregation occurred. Right panel: octameric conformation of building blocks buried in the RNA-binding surface of N-CTDs. It hindered the formation of filamentous ribonucleocapsids.