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

Meghna Gupta(University of California, San Francisco), Caleigh M. Azumaya(University of California, San Francisco), Michelle Moritz(University of California, San Francisco), Sergei Pourmal(University of California, San Francisco), Amy Diallo(University of California, San Francisco), Gregory E. Merz(University of California, San Francisco), Gwendolyn Μ. Jang(Gladstone Institutes), Mehdi Bouhaddou(Gladstone Institutes), Andrea Fossati(Gladstone Institutes), Axel F. Brilot(University of California, San Francisco), Devan Diwanji(University of California, San Francisco), Evelyn Hernandez(University of California, San Francisco), Nadia Herrera(University of California, San Francisco), Huong T. Kratochvil(University of California, San Francisco), Victor L. Lam(University of California, San Francisco), Fei Li(University of California, San Francisco), Yang Li(University of California, San Francisco), Henry C. Nguyen(University of California, San Francisco), Carlos Nowotny(University of California, San Francisco), Tristan W. Owens(University of California, San Francisco), Jessica K. Peters(University of California, San Francisco), Alexandrea N. Rizo(University of California, San Francisco), Ursula Schulze‐Gahmen(University of California, San Francisco), Amber M. Smith(University of California, San Francisco), I.D. Young(University of California, San Francisco), Zanlin Yu(University of California, San Francisco), Daniel Asarnow(University of California, San Francisco), Christian B. Billesbølle(University of California, San Francisco), Melody G. Campbell(Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa), Jen Chen(University of California, San Francisco), Kuei‐Ho Chen(Gladstone Institutes), Un Seng Chio(University of California, San Francisco), Miles Sasha Dickinson(University of California, San Francisco), Loan Doan(University of California, San Francisco), Mingliang Jin(University of California, San Francisco), Kate Kim(University of California, San Francisco), Junrui Li(University of California, San Francisco), Yen-Li Li(University of California, San Francisco), Edmond M. Linossi(University of California, San Francisco), Yanxin Liu(University of California, San Francisco), Megan Lo(University of California, San Francisco), Jocelyne Lopez(University of California, San Francisco), Kyle E. Lopez(University of California, San Francisco), Adamo Mancino(University of California, San Francisco), Frank R. Moss(University of California, San Francisco), Michael Paul(University of California, San Francisco), Komal Ishwar Pawar(University of California, San Francisco), Adrian Pelin(Gladstone Institutes), Thomas H. Pospiech(University of California, San Francisco), Cristina Puchades(University of California, San Francisco), Soumya G. Remesh(University of California, San Francisco), Maliheh Safari(University of California, San Francisco), Kaitlin Schaefer(University of California, San Francisco), Ming Sun(University of California, San Francisco), Mariano Tabios(University of California, San Francisco), Aye C. Thwin(University of California, San Francisco), Erron W. Titus(University of California, San Francisco), Raphael Trenker(University of California, San Francisco), Eric Tse(University of California, San Francisco), Tsz Kin Martin Tsui(University of California, San Francisco), Feng Wang(University of California, San Francisco), Kaihua Zhang(University of California, San Francisco), Sunny Zhang(University of California, San Francisco), Jianhua Zhao(University of California, San Francisco), Fengbo Zhou(University of California, San Francisco), Yuan Zhou(Gladstone Institutes), Lorena Zuliani‐Alvarez(Gladstone Institutes), David A. Agard(University of California, San Francisco), Yifan Cheng(Howard Hughes Medical Institute), James S. Fraser(University of California, San Francisco), Natalia Jura(University of California, San Francisco), Tanja Kortemme(University of California, San Francisco), Aashish Manglik(University of California, San Francisco), Daniel R. Southworth(University of California, San Francisco), Robert M. Stroud(University of California, San Francisco), Danielle L. Swaney(Gladstone Institutes), Nevan J. Krogan(Gladstone Institutes), Adam Frost(University of California, San Francisco), Oren S. Rosenberg(University of California, San Francisco), Kliment A. Verba(University of California, San Francisco)
bioRxiv (Cold Spring Harbor Laboratory)
May 12, 2021
10.1101/2021.05.10.443524
Cited by 84Open Access
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Abstract

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.

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