The 3D structure of the influenza virus polymerase complex was determined by electron microscopy and image processing of recombinant ribonucleoproteins (RNPs). The RNPs were generated by in vivo amplification using cDNAs of the three polymerase subunits, the nucleoprotein, and a model virus-associated RNA containing 248 nt. The polymerase structure obtained is very compact, with no apparent boundaries among subunits. The position of specific regions of the PB1, PB2, and PA subunits was determined by 3D reconstruction of either RNP-mAb complexes or tagged RNPs. This structural model is available for the polymerase of a negative-stranded RNA virus and provides a general delineation of the complex and its interaction with the template-associated nucleoprotein monomers in the RNP.M any viruses contain RNA as genetic material and use RNA-dependent RNA polymerases as enzymes for replication and transcription. The atomic structures of several viral RNA (vRNA)-dependent RNA polymerases from positive-and double-stranded RNA viruses are available (1-6). These proteins show little sequence homology with other DNA-dependent polymerases but contain specific sequence motifs shared with other polymerases (7). They show a typical right-hand fold that includes the thumb, finger, and palm domains, the last of which contains the conserved sequence motifs involved in polymerase catalysis. These polymerases are medium-size proteins that show activity in vitro, although viral replication and transcription in vivo are carried out by polymerase-containing macrocomplexes. In these, other viral and cellular factors contribute to the efficiency and regulation of the polymerase or to the localization of the RNA synthetic machinery in the infected cell (reviewed in ref. 8).The situation in negative-strand viruses (NSVs) is different. The templates for transcription and replication are ribonucleoproteins (RNPs) in which the negative-stranded RNA is complexed with the nucleoprotein (NP) and associated to the polymerase. In the NSVs, the polymerase is a very large protein, the L protein (Ϸ 250 kDa, except in the Orthomyxoviridae), which consists of a heterotrimer of similar aggregate size. The replication intermediates are RNPs similar to virion RNPs but containing positive-stranded RNA. Other viral proteins, such as the P protein for nonsegmented NSVs, and cellular factors are essential for transcription or replication of NSV RNPs. As a consequence of this complexity, very little structural information is available on NSV polymerases.Within the NSVs, influenza A viruses are distinct in having a segmented genome and replicating in the cell nucleus (9). Their genome consists of eight RNPs that are transcribed and replicated by the viral polymerase, a heterotrimer composed by the PB1, PB2, and PA subunits (10, 11). Replication of vRNA involves de novo initiation of nascent RNA chains, whereas initiation of mRNA synthesis requires the generation of capped primers from cellular heterogeneous nuclear RNAs by a capstealing mechanism (12). Transcript...