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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 health1. Elucidation of the underlying mechanisms of viral replication is critical for development of anti-influenza virus drugs2. 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 binding3,4; PA is implicated in RNA replication5,6,7,8,9,10 and proteolytic activity11,12,13,14, although its function is less clearly defined. Here we report the 2.9 ångström structure of avian H5N1 influenza A virus PA (PAC, residues 257–716) in complex with the PA-binding region of PB1 (PB1N, residues 1–25). PAC has a fold resembling a dragon’s head with PB1N clamped into its open ‘jaws’. PB1N is a known inhibitor that blocks assembly of the polymerase heterotrimer and abolishes viral replication. Our structure provides details for the binding of PB1N to PAC 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 PAC with the λ3 reovirus polymerase structure, and docking the PAC structure into an available low resolution electron microscopy map.

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Figure 1: The PA C –PB1 N complex structure.
Figure 2: Representations of the PA C groove and channel.
Figure 3: Model of the influenza polymerase heterotrimer.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structure have been deposited in the Protein Data Bank under accession number 3CM8.


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We thank H. Chen and K. Yu for providing the A/goose/Guangdong/1/96 influenza PA gene; J. Ortin and O. Llorca for supplying electron microscopy maps; C. Yang, X. Su, F. Sun, L. Wang and R.-M. Xu for advice and technical assistance; and S. Harrison, P. Kuhn, X. Chen and T. Toyoda for discussion. This work was supported by the National Natural Science Foundation of China (grant numbers 30599432 and 30221003), the Ministry of Science and Technology International Cooperation Project (grant number 2006DFB32420), the Ministry of Science and Technology 863 Project (grant numbers 2006AA02A314 and 2006AA02A322) and the Ministry of Science and Technology 973 Project (grant numbers 2006CB504300 and 2007CB914300).

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Correspondence to Zihe Rao or Yingfang Liu.

Supplementary information

The file contains Supplementary Figures and Legends S1-S5; Supplementary Tables T1 and T2.

The Supplementary Figures show a multiple sequence alignment for PAC and PB1N (S1), representative electron density (S2) and known mutation sites for the PAC structure (S3), together with in vitro binding assays for PB1N to several double-point mutants of PAC (S4) and a superposition between structures of PAC and λ3 reovirus polymerase N-terminal domain (S5). The Supplementary Table T1 includes data collection, phasing and refinement statistics for PAC:PB1N. The Supplementary Table T2 includes a prediction of the effects of several known mutations in PAC. (PDF 670 kb)

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He, X., Zhou, J., Bartlam, M. et al. Crystal structure of the polymerase PAC–PB1N complex from an avian influenza H5N1 virus. Nature 454, 1123–1126 (2008).

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