8TFD

Crystal structure of a stem-loop DNA aptamer complexed with SARS-CoV-2 nucleocapsid protein RNA-binding domain

Summary for 8TFD

• Entry DOI: 10.2210/pdb8tfd/pdb
• Descriptor: Nucleoprotein, DNA aptamer, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: dna binding protein, endonuclease, replication, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV, SARS-CoV-2); More
• Total number of polymer chains: 2
• Total formula weight: 20792.26

Authors

Esler, M.,Belica, C.,Shi, K.,Aihara, H. (deposition date: 2023-07-10, release date: 2024-11-13, Last modification date: 2024-12-11)

Primary citation

Esler, M.A.,Belica, C.A.,Rollie, J.A.,Brown, W.L.,Moghadasi, S.A.,Shi, K.,Harki, D.A.,Harris, R.S.,Aihara, H.
A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain.
Nucleic Acids Res., 52:13138-13151, 2024

PubMed Abstract: SARS-CoV-2 nucleocapsid (N) protein is a structural component of the virus with essential roles in the replication and packaging of the viral RNA genome. The N protein is also an important target of COVID-19 antigen tests and a promising vaccine candidate along with the spike protein. Here, we report a compact stem-loop DNA aptamer that binds tightly to the N-terminal RNA-binding domain of SARS-CoV-2 N protein. Crystallographic analysis shows that a hexanucleotide DNA motif (5'-TCGGAT-3') of the aptamer fits into a positively charged concave surface of N-NTD and engages essential RNA-binding residues including Tyr109, which mediates a sequence-specific interaction in a uracil-binding pocket. Avid binding of the DNA aptamer allows isolation and sensitive detection of full-length N protein from crude cell lysates, demonstrating its selectivity and utility in biochemical applications. We further designed a chemically modified DNA aptamer and used it as a probe to examine the interaction of N-NTD with various RNA motifs, which revealed a strong preference for uridine-rich sequences. Our studies provide a high-affinity chemical probe for the SARS-CoV-2 N protein RNA-binding domain, which may be useful for diagnostic applications and investigating novel antiviral agents.

PubMed: 39380503
DOI: 10.1093/nar/gkae874

Experimental method

X-RAY DIFFRACTION (1.55 Å)