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TitleCryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.
Journal, issue, pagesbioRxiv, Year 2021
Publish dateMay 11, 2021
AuthorsMeghna Gupta / Caleigh M Azumaya / Michelle Moritz / Sergei Pourmal / Amy Diallo / Gregory E Merz / Gwendolyn Jang / Mehdi Bouhaddou / Andrea Fossati / Axel F Brilot / Devan Diwanji / Evelyn Hernandez / Nadia Herrera / Huong T Kratochvil / Victor L Lam / Fei Li / Yang Li / Henry C Nguyen / Carlos Nowotny / Tristan W Owens / Jessica K Peters / Alexandrea N Rizo / Ursula Schulze-Gahmen / Amber M Smith / Iris D Young / Zanlin Yu / Daniel Asarnow / Christian Billesbølle / Melody G Campbell / Jen Chen / Kuei-Ho Chen / Un Seng Chio / Miles Sasha Dickinson / Loan Doan / Mingliang Jin / Kate Kim / Junrui Li / Yen-Li Li / Edmond Linossi / Yanxin Liu / Megan Lo / Jocelyne Lopez / Kyle E Lopez / Adamo Mancino / Frank R Moss / Michael D Paul / Komal Ishwar Pawar / Adrian Pelin / Thomas H Pospiech / Cristina Puchades / Soumya Govinda Remesh / Maliheh Safari / Kaitlin Schaefer / Ming Sun / Mariano C Tabios / Aye C Thwin / Erron W Titus / Raphael Trenker / Eric Tse / Tsz Kin Martin Tsui / Feng Wang / Kaihua Zhang / Yang Zhang / Jianhua Zhao / Fengbo Zhou / Yuan Zhou / Lorena Zuliani-Alvarez / / David A Agard / Yifan Cheng / James S Fraser / Natalia Jura / Tanja Kortemme / Aashish Manglik / Daniel R Southworth / Robert M Stroud / Danielle L Swaney / Nevan J Krogan / Adam Frost / Oren S Rosenberg / Kliment A Verba /
PubMed AbstractThe 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 ...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.
External linksbioRxiv / PubMed:34013269 / PubMed Central
MethodsEM (single particle)
Resolution3.15 - 3.76 Å
Structure data

23970

7msw

EMDB-23970, PDB-7msw:
Full length SARS-CoV-2 Nsp2
Method: EM (single particle) / Resolution: 3.76 Å

23971

7msx

EMDB-23971, PDB-7msx:
SARS-CoV-2 Nsp2
Method: EM (single particle) / Resolution: 3.15 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • severe acute respiratory syndrome coronavirus 2
KeywordsVIRAL PROTEIN / Nsp2 / virus infection / SARS-CoV-2 / Orf1a

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