X-ray structure of NS1 from a highly pathogenic H5N1 influenza virus

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The recent emergence of highly pathogenic avian (H5N1) influenza viruses, their epizootic and panzootic nature, and their association with lethal human infections have raised significant global health concerns1,2. Several studies have underlined the importance of non-structural protein NS1 in the increased pathogenicity and virulence of these strains3,4. NS1, which consists of two domains—a double-stranded RNA (dsRNA) binding domain5,6 and the effector domain7, separated through a linker—is an antagonist of antiviral type-I interferon response in the host8,9. Here we report the X-ray structure of the full-length NS1 from an H5N1 strain (A/Vietnam/1203/2004) that was associated with 60% of human deaths in an outbreak in Vietnam1,2. Compared to the individually determined structures of the RNA binding domain and the effector domain from non-H5N1 strains, the RNA binding domain within H5N1 NS1 exhibits modest structural changes, while the H5N1 effector domain shows significant alteration, particularly in the dimeric interface. Although both domains in the full-length NS1 individually participate in dimeric interactions, an unexpected finding is that these interactions result in the formation of a chain of NS1 molecules instead of distinct dimeric units. Three such chains in the crystal interact with one another extensively to form a tubular organization of similar dimensions to that observed in the cryo-electron microscopy images of NS1 in the presence of dsRNA. The tubular oligomeric organization of NS1, in which residues implicated in dsRNA binding face a 20-Å-wide central tunnel, provides a plausible mechanism for how NS1 sequesters varying lengths of dsRNA, to counter cellular antiviral dsRNA response pathways, while simultaneously interacting with other cellular ligands during an infection.

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Figure 1: H5N1 NS1 structure.
Figure 2: RBD and ED dimer formation, and the NS1 chain.
Figure 3: NS1 tubular structure.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structure have been deposited with the Protein Data Bank under the accession number 3EU6.


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We thank P. Palese for providing us clones of A/Vietnam/1203/2004 H5N1 and A/PR8/34 (H1N1) NS1. This work was supported by the NIH (AI36040) and the Robert Welch Foundation (to B.V.V.P.). Z.A.B. acknowledges support from an NIH virology training grant (AI07471). We thank P. Palese, A. Rice, M. Schmid and B. Carrillo for discussions and comments on the manuscript and H. Chen for technical assistance with cryo-EM. We acknowledge the use of cryo-EM facilities at the National Center for Macromolecular Imaging (Baylor College of Medicine) supported by the National Institutes of Health (RR002250 to W. Chiu); we also acknowledge the Center for Advanced Microstructures & Devices (CAMD), Baton Rouge, Los Angeles, and H. Bellamy, and the SBC-CAT 19ID beam line at the Advanced Photon Source (supported by the US Department of Energy, Basic Energy Sciences, Office of Science, under contract no.W-31-109-Eng-38) and its staff for their help during data collection.

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Correspondence to B. V. Venkataram Prasad.

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Bornholdt, Z., Prasad, B. X-ray structure of NS1 from a highly pathogenic H5N1 influenza virus. Nature 456, 985–988 (2008) doi:10.1038/nature07444

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