Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase

Deng, Zengqin; Lehmann, Kathleen C.; Li, Xiaorong; Feng, Chong; Wang, Guoqiang; Zhang, Qi; Qi, Xiaoxuan; Yu, Lin; Zhang, Xingliang; Feng, Wenhai; Wu, Wei; Gong, Peng; Tao, Ye; Posthuma, Clara C.; Snijder, Eric J.; Gorbalenya, Alexander E.; Chen, Zhongzhou

To understand how nsp10 unwinds its natural dsRNA substrates, we analysed a complex of nsp10Á with a partially double-stranded DNA substrate. Only seven thymidine residues could be confirmed in the structure of that complex ( Figure 2C ). The DNA-bound nsp10Á structure revealed two possible RNA-binding clefts at the surface of nsp10, which are formed by domains 1B and ZBD (named putative exit site 1), and 1A and ZBD (putative exit site 2), respectively (Supplementary Figure S8) . Both have continuous positively charged surfaces, with the latter (Supplementary Figure S8 , right panel) being sufficiently large to bind a ssRNA >10 bp, which could be especially suited for unwinding complex secondary structures. This organization suggests that, after unwinding, one of the separated RNA chains would be guided through the narrow nucleic acid substrate tunnel formed by domains 1A, 1B and 2A, while the path of the other strand remains to be defined. No matter which cleft is actually used for RNA binding, the positively charged ZBD, and especially its RING-like module, would be involved.