A Resident State Allows Influenza Polymerase to Smoothly Switch between Transcription and Replication Cycles

SUMMARY Influenza polymerase (FluPol) transcripts viral mRNA and switches to replicate viral genome after transcription. However, it remains unknown how FluPol switches between transcription and replication cycles, especially when considering that the structural basis of these two functions is fundamentally different. Here, we proposed a mechanism that FluPol achieves the functional switching between these two cycles through an unreported intermediate conformation, termed as resident state. We obtained a resident state structure of H5N1 FluPol at 3.7 Å using cryo-EM, which is characterized by a blocked Cap-binding domain and a contracted core region, distinct from the structures of either transcription or replication states. Structural analysis results suggest that the resident state structure is feasible to smoothly transit into structures of both transcription and replication states. Furthermore, we show that formation of the resident state is required for both transcription and replication activities of FluPol. Together, the transcription and replication cycles of FluPol are connected via a resident state.