CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

Gupta, Meghna; Azumaya, Caleigh M.; Moritz, Michelle; Pourmal, Sergei; Diallo, Amy; Merz, Gregory E.; Jang, Gwendolyn; Bouhaddou, Mehdi; Fossati, Andrea; Brilot, Axel F.; Diwanji, Devan; Hernandez, Evelyn; Herrera, Nadia; Kratochvil, Huong T.; Lam, Victor L.; Li, Fei; Li, Yang; Nguyen, Henry C.; Nowotny, Carlos; Owens, Tristan W.; Peters, Jessica K.; Rizo, Alexandrea N.; Schulze-Gahmen, Ursula; Smith, Amber M.; Young, Iris D.; Yu, Zanlin; Asarnow, Daniel; Billesbølle, Christian; Campbell, Melody G.; Chen, Jen; Chen, Kuei-Ho; Chio, Un Seng; Dickinson, Miles Sasha; Doan, Loan; Jin, Mingliang; Kim, Kate; Li, Junrui; Li, Yen-Li; Linossi, Edmond; Liu, Yanxin; Lo, Megan; Lopez, Jocelyne; Lopez, Kyle E.; Mancino, Adamo; Moss, Frank R.; Paul, Michael D.; Pawar, Komal Ishwar; Pelin, Adrian; Pospiech, Thomas H.; Puchades, Cristina; Remesh, Soumya Govinda; Safari, Maliheh; Schaefer, Kaitlin; Sun, Ming; Tabios, Mariano C; Thwin, Aye C.; Titus, Erron W.; Trenker, Raphael; Tse, Eric; Tsui, Tsz Kin Martin; Wang, Feng; Zhang, Kaihua; Zhang, Yang; Zhao, Jianhua; Zhou, Fengbo; Zhou, Yuan; Zuliani-Alvarez, Lorena; Agard, David A; Cheng, Yifan; Fraser, James S; Jura, Natalia; Kortemme, Tanja; Manglik, Aashish; Southworth, Daniel R.; Stroud, Robert M; Swaney, Danielle L; Krogan, Nevan J; Frost, Adam; Rosenberg, Oren S; Verba, Kliment A

The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design.