Crystal structure of the polymerase PAC-PB1N complex from an avian influenza H5N1 virus

The recent emergence of highly pathogenic avian influenza A virus strains with subtype H5N1 pose a global threat to human health(1). Elucidation of the underlying mechanisms of viral replication is critical for development of anti- influenza virus drugs(2). The influenza RNA- dependent RNA polymerase ( RdRp) heterotrimer has crucial roles in viral RNA replication and transcription. It contains three proteins: PA, PB1 and PB2. PB1 harbours polymerase and endonuclease activities and PB2 is responsible for cap binding(3,4); PA is implicated in RNA replication(5-10) and proteolytic activity(11-14), although its function is less clearly defined. Here we report the 2.9 angstrom structure of avian H5N1 influenza A virus PA ( PA(C), residues 257 - 716) in complex with the PA- binding region of PB1 ( PB1(N), residues 1 - 25). PA(C) has a fold resembling a dragon's head with PB1(N) clamped into its open 'jaws'. PB1(N) is a known inhibitor that blocks assembly of the polymerase heterotrimer and abolishes viral replication. Our structure provides details for the binding of PB1(N) to PA(C) at the atomic level, demonstrating a potential target for novel anti- influenza therapeutics. We also discuss a potential nucleotide binding site and the roles of some known residues involved in polymerase activity. Furthermore, to explore the role of PA in viral replication and transcription, we propose a model for the influenza RdRp heterotrimer by comparing PA(C) with the lambda 3 reovirus polymerase structure, and docking the PA(C) structure into an available low resolution electron microscopy map.