SARS-CoV-2 is an enveloped virus responsible for the COVID-19 pandemic. Despite recent advances in the structural elucidation of SARS-CoV-2 proteins, the detailed architecture of the intact virus remains to be unveiled. Here we report the molecular assembly of the authentic SARS-CoV-2 virus using cryoelectron tomography (cryo-ET) and subtomogram averaging (STA). Native structures of the S proteins in pre- and postfusion conformations were determined to average resolutions of 8.7–11 Å. Compositions of the N-linked glycans from the native spikes were analyzed by mass spectrometry, which revealed overall processing states of the native glycans highly similar to that of the recombinant glycoprotein glycans. The native conformation of the ribonucleoproteins (RNPs) and their higher-order assemblies were revealed. Overall, these characterizations revealed the architecture of the SARS-CoV-2 virus in exceptional detail and shed light on how the virus packs its ∼30-kb-long single-segmented RNA in the ∼80-nm-diameter lumen.

SARS-CoV-2 是一种导致 COVID-19 大流行的包膜病毒。尽管最近在 SARS-CoV-2 蛋白的结构阐明方面取得了进展，但完整病毒的详细结构仍有待揭开。在这里，我们使用冷冻电子断层扫描 (cryo-ET) 和亚断层扫描平均 (STA) 报告了真正的 SARS-CoV-2 病毒的分子组装。融合前和融合后构象中 S 蛋白的天然结构被确定为平均分辨率为 8.7-11 Å。通过质谱分析天然刺突的 N 连接聚糖的组成，结果表明天然聚糖的整体加工状态与重组糖蛋白聚糖高度相似。揭示了核糖核蛋白（RNP）的天然构象及其高阶组装。总体而言，这些特征非常详细地揭示了 SARS-CoV-2 病毒的结构，并揭示了该病毒如何在直径约 80 nm 的管腔中包装约 30 kb 长的单节段 RNA。