SARS-CoV-2 is the causative agent of the 2019–2020 pandemic. The SARS-CoV-2 genome is replicated and transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp8₂/nsp12) along with a cast of accessory factors. One of these factors is the nsp13 helicase. Both the holo-RdRp and nsp13 are essential for viral replication and are targets for treating the disease COVID-19. Here we present cryoelectron microscopic structures of the SARS-CoV-2 holo-RdRp with an RNA template product in complex with two molecules of the nsp13 helicase. The Nidovirales order-specific N-terminal domains of each nsp13 interact with the N-terminal extension of each copy of nsp8. One nsp13 also contacts the nsp12 thumb. The structure places the nucleic acid-binding ATPase domains of the helicase directly in front of the replicating-transcribing holo-RdRp, constraining models for nsp13 function. We also observe ADP-Mg²⁺ bound in the nsp12 N-terminal nidovirus RdRp-associated nucleotidyltransferase domain, detailing a new pocket for anti-viral therapy development.

SARS-CoV-2 is the causative agent of the 2019–2020 pandemic. The SARS-CoV-2 genome is replicated and transcribed by the RNA-dependent RNA polymerase holoenzyme (subunits nsp7/nsp8₂/nsp12) 以及一系列辅助因素。其中一个因素是 nsp13 解旋酶。holo-RdRp 和 nsp13 都是病毒复制所必需的，并且是治疗 COVID-19 疾病的靶点。在这里，我们展示了 SARS-CoV-2 holo-RdRp 的低温电子显微结构，其 RNA 模板产物与两个 nsp13 解旋酶分子复合。每个 nsp13 的 Nidovirales 顺序特定的 N 末端域与每个 nsp8 副本的 N 末端扩展相互作用。一个 nsp13 还与 nsp12 thumb 联系。该结构将解旋酶的核酸结合 ATPase 结构域直接置于复制-转录全息-RdRp 的前面，从而限制了 nsp13 功能的模型。我们还观察到 ADP-Mg ²⁺结合在 nsp12 N 末端巢状病毒 RdRp 相关核苷酸转移酶结构域中，详细说明了抗病毒治疗开发的新口袋。