Structure of the tilapia lake virus nucleoprotein bound to RNA

Tilapia Lake virus (TiLV) belongs to the Amnoonviridae family within the Articulavirales order of segmented negative-strand RNA viruses and is highly diverged from more familiar orthomyxoviruses, such as influenza. The viral nucleoprotein (NP), a key component of the replication machinery, packages the viral genome into protective ribonucleoprotein particles. Here we describe the electron cryo-microscopy (cryo-EM) structure of TiLV-NP bound to RNA within in vitro reconstituted, small ring-like, pseudo-symmetrical oligomers. Although TiLV-NP is considerably smaller than its influenza counterpart and unrelated in sequence, it maintains the same topology and domain organisation. This comprises a head and body domain between which is a positively charged groove, where single-stranded RNA binds. In addition, an oligomerisation loop inserts into a hydrophobic pocket in the neighbouring NP, the flexible hinges of which allow variable orientation of adjacent NPs. Focused cryo-EM maps unambiguously define the 5' to 3' direction of the bound RNA, confirmed by double stranded, A-form RNA regions that extrude out from some of the NP-NP interfaces. This is the first fully resolved description of how single-stranded and stem-loop RNA binds to an articulaviral NP assembly. Superposition with orthomyxoviral NPs suggest that the mode of RNA binding is likely similar across the Articulavirales order.