Structure of the Nipah virus polymerase complex

Nipah virus poses a recurring threat, causing severe respiratory and neurological disease in Southeast Asia. Since its first identification in Malaysia in 1998 and a subsequent outbreak in Singapore in early 1999, the virus has emerged as a highly virulent zoonotic paramyxovirus. Despite its lethality, there is currently no approved treatment for Nipah virus infection. The viral polymerase complex, composed of the large polymerase protein (L) and the phosphoprotein (P), is responsible for the replication of the viral RNA genome and transcription of viral genes. However, the mechanisms by which the L and P components perform these activities remain unknown. Here, we describe the structures of the Nipah virus L-P polymerase complex at a 2.5 Å resolution and the L protein’s Connecting Domain (CD) at a 1.85 Å resolution, determined by cryo-electron microscopy (cryo-EM) and X-ray crystallography, respectively. The L-P complex structure reveals the organization of the RNA-dependent RNA polymerase (RdRp) and polyribonucleotidyl transferase (PRNTase) domains of the L protein, and how the P protein, which forms a tetramer, interacts with the RdRp domain of the L protein. Furthermore, the CD structure reveals the binding of Mg ions, which likely contribute to the functionality of the PRNTase domain. These findings offer insights into the structural details of the L-P polymerase complex and the molecular interactions between L and P, shedding light on the mechanisms of the replication machinery. This work will underpin efforts to develop antiviral drugs that target the polymerase complex of Nipah virus.