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The mechanism by which influenza A virus nucleoprotein forms oligomers and binds RNA

Nature volume 444, pages 1078–1082 (2006)Cite this article

Abstract

Influenza A viruses pose a serious threat to world public health, particularly the currently circulating avian H5N1 viruses. The influenza viral nucleoprotein forms the protein scaffold of the helical genomic ribonucleoprotein complexes, and has a critical role in viral RNA replication1. Here we report a 3.2 Å crystal structure of this nucleoprotein, the overall shape of which resembles a crescent with a head and a body domain, with a protein fold different compared with that of the rhabdovirus nucleoprotein2,3. Oligomerization of the influenza virus nucleoprotein is mediated by a flexible tail loop that is inserted inside a neighbouring molecule. This flexibility in the tail loop enables the nucleoprotein to form loose polymers as well as rigid helices, both of which are important for nucleoprotein functions. Single residue mutations in the tail loop result in the complete loss of nucleoprotein oligomerization. An RNA-binding groove, which is found between the head and body domains at the exterior of the nucleoprotein oligomer, is lined with highly conserved basic residues widely distributed in the primary sequence. The nucleoprotein structure shows that only one of two proposed nuclear localization signals are accessible, and suggests that the body domain of nucleoprotein contains the binding site for the viral polymerase. Our results identify the tail loop binding pocket as a potential target for antiviral development.

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Figure 1: Nucleoprotein oligomerization behaviour shown by chromatogram.
Figure 2: Electron microscopy images of influenza virus nucleoprotein (strain A/WSN/33).
Figure 3: Nucleoprotein crystal structure.
Figure 4: Inter-subunit interactions mediated by the tail loop.
Figure 5: RNA-binding by nucleoprotein.

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Acknowledgements

We thank V. Vikharia for providing the baculovirus for expressing nucleoprotein from influenza virus A/Hong Kong/1074/99 (H9N2); Z. Xie for electron microscopy analysis; P. Sliz for collecting the nucleoprotein native data; Y. Shamoo and G. Wu for providing the 24-nucleotide ssRNA; and Y. Shamoo, D. Mata and S. Harrison for discussions and critical reading of the manuscript. Nucleoprotein diffraction data were collected at the Brookhaven National Synchrotron Light Source and the Cornell High Energy Synchrotron Source. This work is supported by grants from the Welch Foundation (to Y.J.T and R.M.K), National Institutes of Health (to Y.J.T), and the Nanoscale Science and Engineering Initiative of the National Science Foundation. Author Contributions Q.Y. crystallized the nucleoprotein. Q.Y. and Y.J.T solved the nucleoprotein crystal structure. Y.J.T, Q.Y. and R.M.K. wrote the paper. All authors discussed the results and commented on the manuscript. The coordinates and the structure factor files have been deposited in the Protein Data Bank under accession code 2IQH.

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Authors and Affiliations

  1. Department of Biochemistry and Cell Biology, Rice University, 6100 Main Street, MS140, Texas, 77005, Houston, USA

    Qiaozhen Ye & Yizhi Jane Tao

  2. Institute for Cellular and Molecular Biology, University of Texas at Austin, 2500 Speedway, Texas, 78712-1095, Austin, USA

    Robert M. Krug

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Correspondence to Yizhi Jane Tao.

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The coordinates and the structure factor files have been deposited in the Protein Data Bank under accession code 2IQH. Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.

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Suplementary Information

The file contains Figures 1-5. Figure 1 shows experimental electron density maps of NP, Figure 2 shows a stereo diagram of NP, Figure 3 shows RNA binding activity of the influenza A/WSN/33 NP protein, Table 1 shows diffraction data statistics and Table 2 shows inter-subunit interactions of NP molecules in an NCS trimer.

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Ye, Q., Krug, R. & Tao, Y. The mechanism by which influenza A virus nucleoprotein forms oligomers and binds RNA. Nature 444, 1078–1082 (2006). https://doi.org/10.1038/nature05379

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