CryoEM structure of the Nipah virus nucleocapsid assembly

Nipah virus is a highly pathogenic zoonotic RNA virus, causing fatal encephalitis in humans. Like other negative-strand RNA viruses including Ebola and measles, its genome is wrapped by the nucleocapsid (N) protein forming a helical assembly. Here we report the CryoEM structure of the Nipah nucleocapsid protein-RNA assembly, at near atomic resolution. The N protein wraps the RNA genome with a periodicity of six nucleotides per protomer, around the outer edge of the helical assembly, in common with other paramyxoviruses. This structure uncovers details of the nucleocapsid assembly, demonstrating the role of the N-terminal arm of the N protein in the formation of the helical assembly and revealing details of the sequence-independent coordination of RNA binding in the “3-bases-in, 3-bases-out” conformation. CryoEM analysis also reveals formation of clam-shaped assemblies of the N-protein, mediated by intersubunit interactions involving several N protein loop regions.