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

Gupta, M.; Azumaya, C. M.; Moritz, M.; Pourmal, S.; Diallo, A.; Merz, G. E.; Jang, G. M.; Bouhaddou, M.; Fossati, A.; Brilot, A. F.; Diwanji, D.; Hernandez, E.; Herrera, N.; Kratochvil, H. T.; Lam, V. L.; Li, F.; Li, Y.; Nguyen, H. C.; Nowotny, C.; Owens, T. W.; Peters, J. K.; Rizo, A. N.; Schulze-Gahmen, U.; Smith, A. M.; Young, I. D.; Yu, Z.; Asarnow, D.; Billesbolle, C.; Campbell, M. G.; Chen, J.; Chen, K.-H.; Chio, U. S.; Dickinson, M. S.; Doan, L.; Jin, M.; Kim, K.; Li, J.; Li, Y.-L.; Linossi, E.; Liu, Y.; Lo, M.; Lopez, J.; Lopez, K. E.; Mancino, A.; Moss, F. R.; Paul, M. D.; Pawar, K. I

doi:10.1101/2021.05.10.443524

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bioRxiv · 10.1101/2021.05.10.443524

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

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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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Gupta, M., Azumaya, C. M., Moritz, M., Pourmal, S., Diallo, A., Merz, G. E., Jang, G. M., Bouhaddou, M., Fossati, A., Brilot, A. F., Diwanji, D., Hernandez, E., Herrera, N., Kratochvil, H. T., Lam, V. L., Li, F., Li, Y., Nguyen, H. C., Nowotny, C., Owens, T. W., Peters, J. K., Rizo, A. N., Schulze-Gahmen, U., Smith, A. M., Young, I. D., Yu, Z., Asarnow, D., Billesbolle, C., Campbell, M. G., Chen, J., Chen, K.-H., Chio, U. S., Dickinson, M. S., Doan, L., Jin, M., Kim, K., Li, J., Li, Y.-L., Linossi, E., Liu, Y., Lo, M., Lopez, J., Lopez, K. E., Mancino, A., Moss, F. R., Paul, M. D., Pawar, K. I. 2021-05-12. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.. https://doi.org/10.1101/2021.05.10.443524

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