Figure 4.

SAXS structures of unliganded MDA5 fragments. (A) DA model of the MDA5 helicase domains. (B) Homology model of the Hel1, Hel2i and Hel2 helicase domains (light to dark grey, respectively) refined against the SAXS curve. The helix between Hel2 and the CTD (Hel-link; yellow) was docked manually prior to refinement. The envelope of the DA model is shown superimposed. (C) DA model of CARD-deleted MDA5 with the additional lobe corresponding to the CTD in cyan. (D) Superposition of the six best rigid-body models of CARD-deleted MDA5 consistent with the SAXS data. Coloured regions were constrained by flexible loops; the helicase domains (grey) were fixed. The positions of the CTDs are indicated by ovals and a representative cartoon (cyan). (E) DA model of the CARDs. All DA models represent an average of 15 models. (F) Calculated one-dimensional X-ray scattering of MDA5 CARD homology models in prototypical death domain family interactions (red and blue) fitted against the observed scattering (black). The ‘b’ indicates a swap of the two CARD domains across the interface. The curves were vertically offset for clarity and the best fit is indicated in blue. (G) Cartoon representation of the CARD homology model with the type II interface (blue to red, N- to C-terminus). See also Supplementary Figure S3 and Supplementary Table SII.