7F2B

Crystal structure of SARS-CoV-2 nucleocapsid protein C-terminal RNA binding domain at 2.0A resolution

Summary for 7F2B

• Entry DOI: 10.2210/pdb7f2b/pdb
• Descriptor: Nucleoprotein, PHOSPHATE ION, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: sars-cov-2, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2)
• Total number of polymer chains: 2
• Total formula weight: 24626.27

Authors

Liu, C.,Chen, Y.W. (deposition date: 2021-06-10, release date: 2021-09-01, Last modification date: 2023-11-29)

Primary citation

Jia, Z.,Liu, C.,Chen, Y.,Jiang, H.,Wang, Z.,Yao, J.,Yang, J.,Zhu, J.,Zhang, B.,Yuchi, Z.
Crystal structures of the SARS-CoV-2 nucleocapsid protein C-terminal domain and development of nucleocapsid-targeting nanobodies.
Febs J., 289:3813-3825, 2022

PubMed Abstract: The ongoing outbreak of COVID-19 caused by SARS-CoV-2 has resulted in a serious public health threat globally. Nucleocapsid protein is a major structural protein of SARS-CoV-2 that plays important roles in the viral RNA packing, replication, assembly, and infection. Here, we report two crystal structures of nucleocapsid protein C-terminal domain (CTD) at resolutions of 2.0 Å and 3.1 Å, respectively. These two structures, crystallized under different conditions, contain 2 and 12 CTDs in asymmetric unit, respectively. Interestingly, despite different crystal packing, both structures show a similar dimeric form as the smallest unit, consistent with its solution form measured by the size-exclusion chromatography, suggesting an important role of CTD in the dimerization of nucleocapsid proteins. By analyzing the surface charge distribution, we identified a stretch of positively charged residues between Lys257 and Arg262 that are involved in RNA-binding. Through screening a single-domain antibodies (sdAbs) library, we identified four sdAbs targeting different regions of nucleocapsid protein with high affinities that have future potential to be used in viral detection and therapeutic purposes.

PubMed: 34665939
DOI: 10.1111/febs.16239

Experimental method

X-RAY DIFFRACTION (2 Å)