Non-structural protein 5 (NS5) is the largest and most highly conserved central component within the replication complex of flaviviruses. It is a multifunctional enzyme containing melthyltransferase (MTase), and RNA-dependent RNA-polymerase (RdRp) activities that are essential for viral RNA replication. To-date, despite the determination of crystal structures of isolated NS5 domains, critical questions regarding the cross-talk between N-terminal MTase domain and C- terminal RdRp domain are still elusive. Additionally, the impact of linker, which physically connects two domains, on the mechanism of the functions has not been fully investigated. We have obtained the first 3D structure of the full-length dengue virus serotype 3 (DENV3) NS5 protein which is distinct from the full-length structure of Japanese encephalitis virus (JEV) despite their common flaviviral membership. The DENV3 NS5 solved to a resolution of 2.3 Å is complexed with S-adenosyl-L-homocysteine (SAH) and GTP, and it shows two clusters of electrostatic-rich interface.  Moreover a well-ordered linker region consisting of a short 3₁₀ helix is revealed, which may function as a conformational switch to accommodate the multifunctional activities of NS5 during different stages of viral replication. The structure and activity of DENV NS5 will be discussed and the role of specific interdomain interactions in the cross-talk will be dissected using reverse genetics.