7VNU

Crystal structure of the N-terminal domain of SARS-CoV-2 nucleocapsid protein

Summary for 7VNU

• Entry DOI: 10.2210/pdb7vnu/pdb
• Descriptor: Nucleoprotein, ACETATE ION (3 entities in total)
• Functional Keywords: coronavirus, nucleocapsid, viral protein., viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2)
• Total number of polymer chains: 4
• Total formula weight: 57322.66

Authors

Zhou, R.J.,Ni, X.C.,Lei, J. (deposition date: 2021-10-12, release date: 2021-10-27, Last modification date: 2023-11-29)

Primary citation

Ni, X.,Han, Y.,Zhou, R.,Zhou, Y.,Lei, J.
Structural insights into ribonucleoprotein dissociation by nucleocapsid protein interacting with non-structural protein 3 in SARS-CoV-2.
Commun Biol, 6:193-193, 2023

PubMed Abstract: The coronavirus nucleocapsid (N) protein interacts with non-structural protein 3 (Nsp3) to facilitate viral RNA synthesis and stabilization. However, structural information on the N-Nsp3 complex is limited. Here, we report a 2.6 Å crystal structure of the N-terminal domain (NTD) of the N protein in complex with the ubiquitin-like domain 1 (Ubl1) of Nsp3 in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One NTD and two Ubl1s formed a stable heterotrimer. We performed mutational analysis to reveal the key residues for this interaction. We confirmed the colocalization of SARS-CoV-2 N and Nsp3 in Huh-7 cells. N-Ubl1 interaction also exists in SARS-CoV and Middle East respiratory syndrome coronavirus. We found that SARS-CoV-2 Ubl1 competes with RNA to bind N protein in a dose-dependent manner. Based on our results, we propose a model for viral ribonucleoprotein dissociation through N protein binding to Ubl1 of Nsp3.

PubMed: 36806252
DOI: 10.1038/s42003-023-04570-2

Experimental method

X-RAY DIFFRACTION (1.95 Å)