MERS-CoV ORF4b employs an unusual binding mechanism to target IMPα and block innate immunity

MERS-CoV ORF4b antagonizes host innate immune response, partially via blocking nuclear import adapter IMP alpha activity and preventing nuclear translocation of NF-kappa B. Here, Munasinghe and Edwards et al. biochemically and structurally define the interaction between ORF4b and IMP alpha-family members and find a non-canonical interaction between ORF4b NLS and IMP alpha 2 and IMP alpha 3. The MERS coronavirus (MERS-CoV) is a highly pathogenic, emerging virus that produces accessory proteins to antagonize the host innate immune response. The MERS-CoV ORF4b protein has been shown to bind preferentially to the nuclear import adapter IMP alpha 3 in infected cells, thereby inhibiting NF-kappa B-dependent innate immune responses. Here, we report high-resolution structures of ORF4b bound to two distinct IMP alpha family members. Each exhibit highly similar binding mechanisms that, in both cases, lack a prototypical Lys bound at their P2 site. Mutations within the NLS region dramatically alter the mechanism of binding, which reverts to the canonical P2 Lys binding mechanism. Mutational studies confirm that the novel binding mechanism is important for its nuclear import, IMP alpha interaction, and inhibition of innate immune signaling pathways. In parallel, we determined structures of the nuclear binding domain of NF-kappa B component p50 bound to both IMP alpha 2 and alpha 3, demonstrating that p50 overlaps with the ORF4b binding sites, suggesting a basis for inhibition. Our results provide a detailed structural basis that explains how a virus can target the IMP alpha nuclear import adapter to impair immunity, and illustrate how small mutations in ORF4b, like those found in closely related coronaviruses such as HKU5, change the IMP alpha binding mechanism.

Automated summary

In this study, the authors biochemically and structurally characterized the interaction between MERS-CoV ORF4b and IMP alpha-family members. They found that mutations in ORF4b alter its binding mechanism with IMP alpha, which impairs nuclear import, interaction with IMP alpha, and inhibition of immune signaling pathways. The study also revealed that the binding sites of NF-kappa B component p50 and ORF4b overlap, suggesting a possible mechanism for inhibition.