Abstact

In positive-strand RNA viruses, the genome serves as a template for both protein translation and negative-strand RNA synthesis. Enteroviruses use the cloverleaf RNA structure at the 5' end of the genome to balance these two processes. Cloverleaf acts as a promoter for RNA synthesis and forms a complex with viral 3CD protein, the precursor to 3Cpro protease, and 3Dpol polymerase. The interaction between cloverleaf and 3CD is mediated by the 3Cpro domain, yet how 3Cpro promotes specific RNA-binding is not clear. We report the structure of coxsackievirus cloverleaf RNA-3Cpro complex, wherein two 3Cpro molecules interact with cloverleaf stem-loop D. 3Cpro dimer mainly recognizes the shape of the dsRNA helix through symmetric interactions, suggesting that 3Cpro is a previously undiscovered type of RNA binding protein. We show that 3CD protein also dimerizes on cloverleaf RNA and binds the RNA with higher affinity than 3Cpro. The structure provides insight into the RNA-binding mechanism of 3Cpro or 3CD with other cis-acting replication elements.