Volume 23, Issue 11, Pages 2001-2010 (November 2015) Structural Basis for a Novel Interaction between the NS1 Protein Derived from the 1918 Influenza Virus and RIG-I  Alexander S. Jureka, Alex B. Kleinpeter, Gabriel Cornilescu, Claudia C. Cornilescu, Chad M. Petit  Structure  Volume 23, Issue 11, Pages 2001-2010 (November 2015) DOI: 10.1016/j.str.2015.08.007 Copyright © 2015 Elsevier Ltd Terms and Conditions

Structure 2015 23, 2001-2010DOI: (10.1016/j.str.2015.08.007) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 1 1H-15N HSQC Spectra of the 1918H1N1 NS1RBD with Residue-Specific Backbone Assignments Indicated Structure 2015 23, 2001-2010DOI: (10.1016/j.str.2015.08.007) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 2 NMR Chemical Shift Perturbations Reveal an Interaction between the 1918H1N1 NS1RBD and the Second CARD Domain of RIG-I (A) Overlay of 1H-15N HSQC spectra of the 1918H1N1 NS1RBD (black) and the 1918H1N1 NS1RBD after adding unlabeled CARD2 (purple) at a 1:1 molar ratio. (B) Chemical shift perturbations (CSPs) were quantified and plotted on a per-residue basis. The dotted line represents the calculated 2σ0corr cutoff (0.024 ppm) with those residues experiencing shifts greater than the cutoff highlighted in purple (see Experimental Procedures). Structure 2015 23, 2001-2010DOI: (10.1016/j.str.2015.08.007) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 3 NMR CSP Demonstrates No Discernible Interaction between the Udorn NS1RBD and the Second CARD Domain of RIG-I Overlay of 1H-15N HSQC spectra of the Udorn NS1RBD (black) and in the presence of CARD2 (cyan) indicate no CSPs upon the addition of unlabeled CARD2 at a 1:1 molar ratio. Structure 2015 23, 2001-2010DOI: (10.1016/j.str.2015.08.007) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 4 Alignment of the 1918H1N1 and Udorn NS1RBD Residues that are not conserved between the two strains are outlined in gray. Structure 2015 23, 2001-2010DOI: (10.1016/j.str.2015.08.007) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 5 Solution NMR Structural Studies of the 1918H1N1 NS1RBD (A) Ribbon diagram of the 16 energy-minimized conformers that represent the NMR structure of the 1918H1N1 NS1RBD (1–73) homodimer. The two monomers are shown in black and green, respectively, with the N and C termini labeled for each. (B) Monomeric structure with residues that are mutated when comparing the 1918H1N1 NS1RBD with the Udorn NS1RBD (indicated in blue). (C) Multiple views of the 1918H1N1 NS1RBD, indicating that it retains the canonical six-helical fold demonstrated by previously solved solution structure of the influenza Udorn NS1RBD. Structure 2015 23, 2001-2010DOI: (10.1016/j.str.2015.08.007) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 6 CSPs Induced by the Addition of CARD2 Reveal a Functionally Novel Region of the NS1RBD Perturbations are mapped onto the lowest-energy structure of the 1918H1N1 NS1RBD with shifts greater than 2σ0corr shown in purple. Helices known to be involved in RNA binding (blue) exist opposite to the identified CARD2 binding interface. Structure 2015 23, 2001-2010DOI: (10.1016/j.str.2015.08.007) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 7 Prospective Salt Bridge Alters the Orientation of α3 and α3′ and May Facilitate Strain Specificity (A) Alignment of the ensemble Udorn NS1RBD (cyan) and 1918H1N1 NS1RBD (purple) structures. (B) Ribbon diagram of the 1918H1N1 NS1RBD, with residues involved in the potential salt bridges labeled and the distances between them indicated. Structure 2015 23, 2001-2010DOI: (10.1016/j.str.2015.08.007) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 8 NMR CSP Demonstrates No Discernible Interaction between the 1918H1N1 NS1RBD R21Q and the Second CARD Domain of RIG-I Overlay of 1H-15N HSQC spectra of the 1918H1N1 NS1RBD R21Q (black) and in the presence of CARD2 (green) indicate no CSPs upon the addition of unlabeled CARD2 at a 1:1 molar ratio. Structure 2015 23, 2001-2010DOI: (10.1016/j.str.2015.08.007) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 9 Quantitative Structural Analysis Reveals Differences in the Relative Spatial Arrangements of the α3 and α3′ Helices from the 1918H1N1 and Udorn NS1RBD (A) Clustal alignment of the 1918H1N1 and Udorn NS1RBD, with residue differences indicated in gray. (B–E) Comparison of the distances between the 1918H1N1 α3 and α3′ Cα atoms (B), atoms composing the peptidyl backbone (C), atoms composing the side chains (D), and all atoms (E) demonstrate a significant difference in the average distance between the α3 and α3′ helices from the in the 1918H1N1 NS1RBD compared with the Udorn NS1RBD. The resultant data were analyzed using the Student t test and all data are represented as the mean ± SEM. Structure 2015 23, 2001-2010DOI: (10.1016/j.str.2015.08.007) Copyright © 2015 Elsevier Ltd Terms and Conditions

Figure 10 Sequence Logo Displaying the Conservation of Residues in the Regions of the NS1RBD that Interact with CARD2 Sequence alignment was performed on all NS1 sequences (8,828) found in the influenza database (www.fludb.org). This figure was generated using WebLogo (Crooks et al., 2004). Structure 2015 23, 2001-2010DOI: (10.1016/j.str.2015.08.007) Copyright © 2015 Elsevier Ltd Terms and Conditions