Structural insights into Crimean-Congo haemorrhagic fever virus RNA polymerase reveal a dual-site non-nucleoside inhibition mechanism

Abstract

Crimean-Congo hemorrhagic fever virus (CCHFV) is a priority pathogen defined by its wide geographic distribution and high case-fatality rates, yet no approved vaccines or therapeutics exist. Its massive ~450 kDa RNA-dependent RNA polymerase (L protein)—the multi-domain and multi-functional machinery for viral transcription and replication—has remained structurally enigmatic due to its exceptional size and complexity. Here we present cryo-EM structures of the CCHFV L protein in apo, promoter-bound, and inhibitor-bound states. Structural analysis reveals that the L protein adopts the canonical architecture shared across the order Bunyavirales, with high structural conservation extending to individual subdomains and the 'hook-like' recognition of the vRNA promoter. Unexpectedly, we found that the non-nucleotide inhibitor suramin inhibits the polymerase through a unique dual-site mechanism. It not only competitively occludes the 5' vRNA-binding pocket but also functions as a “molecular glue” at the distal Linker–Fingers interface, likely allosterically restricting essential conformational dynamics. These findings provide a detailed structural framework for CCHFV replication and offer a novel paradigm for designing antivirals against Bunyavirales.