Protein Structure and Folding
Conserved Surface Features Form the Double-stranded RNA Binding Site of Non-structural Protein 1 (NS1) from Influenza A and B Viruses*

https://doi.org/10.1074/jbc.M611619200Get rights and content
Under a Creative Commons license
open access

Influenza A viruses cause a highly contagious respiratory disease in humans and are responsible for periodic widespread epidemics with high mortality rates. The influenza A virus NS1 protein (NS1A) plays a key role in countering host antiviral defense and in virulence. The 73-residue N-terminal domain of NS1A (NS1A-(1–73)) forms a symmetric homodimer with a unique six-helical chain fold. It binds canonical A-form double-stranded RNA (dsRNA). Mutational inactivation of this dsRNA binding activity of NS1A highly attenuates virus replication. Here, we have characterized the unique structural features of the dsRNA binding surface of NS1A-(1–73) using NMR methods and describe the 2.1-Å x-ray crystal structure of the corresponding dsRNA binding domain from human influenza B virus NS1B-(15–93). These results identify conserved dsRNA binding surfaces on both NS1A-(1–73) and NS1B-(15–93) that are very different from those indicated in earlier “working models” of the complex between dsRNA and NS1A-(1–73). The combined NMR and crystallographic data reveal highly conserved surface tracks of basic and hydrophilic residues that interact with dsRNA. These tracks are structurally complementary to the polyphosphate backbone conformation of A-form dsRNA and run at an ∼45° angle relative to the axes of helices α2/α2′. At the center of this dsRNA binding epitope, and common to NS1 proteins from influenza A and B viruses, is a deep pocket that includes both hydrophilic and hydrophobic amino acids. This pocket provides a target on the surface of the NS1 protein that is potentially suitable for the development of antiviral drugs targeting both influenza A and B viruses.

Cited by (0)

The atomic coordinates and structure factors (code 1xeq) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

*

This work was supported by National Institutes of Health Protein Structure Initiative Grants U54 GM074958 (to G. T. M.), AI49475 (to L. T.), and AI11772 (to R. M. K.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. S1–S5 and Table S-I.

1

These authors contributed equally to this work.

2

A graduate fellow of the Biological, Mathematical, and Physical Sciences (BioMAPS) program at Rutgers University.