Crystal structures of RNA-dependent RNA polymerases from Jingmen tick virus and Alongshan virus

Jingmenviruses are a group of flavi-like viruses with segmented genome and have been found in various types of hosts, including humans, cattle, monkeys, bats, rodents, sheep, ticks, mosquitoes and nematodes. Jingmenviruses, including the Jingmen tick virus (JMTV) and Alongshan virus (ALSV), have been associated with febrile illness and flu-like symptoms in humans. Viral polymerase plays critical roles in genome replication and transcription and is an ideal target for antiviral drugs. Here, we determined the crystal structures of RNA-dependent RNA polymerase (RdRp) domains of JMTV and ALSV at 2.6 Å and 3.2 Å resolutions, respectively. The overall structures of JMTV and ALSV RdRp domains are similar to those from the typical unsegmented viruses in Flaviviridae family, especially the Flavivirus genus. JMTV and ALSV RdRps can be divided into three subdomains and the catalytical Motif A-G are conserved like the typical flaviviruses, whereas the zinc-binding pockets are absent from the JMTV and ALSV RdRps. The 5′-ends of jingmenvirus genomes are varied in length and sequence, and a highly conserved 8-nucleotide element located on the tip of stem loop A was identified and shown to be required for binding with RdRp and performing de novo replication activity. These findings provide important structural insights into RdRp of segmented flavivirus and reveal the key region of virus genome responsible for replication initiation, which would promote molecular understanding of segmented flavivirus replication and the structure-based design of antiviral drugs against flaviviruses.