Figure 1 Three dimensional models of the SARS-CoV-2 virion and a schematic diagram of its four structural proteins. Figures were modified from coronavirusexplained
A novel zoonotic coronavirus SARS-CoV-2 was originally explored in Wuhan, China in December 2019 and further regarded to the serious pandemic known as COVID-19. In early March 2022, the global COVID-19 pandemic has caused over 453 million confirmed cases and over 6 million deaths (John Hopkins Coronavirus Resource Center, https://coronavirus.jhu.edu).
The COVID-19 virus and the emergence of new virus variants seriously threat to global public health. It is a strong requirement to develop the effective diagnostic tools which are able to quickly and reliably detect active SARS-CoV-2 infections.
Structural proteins of the COVID-19 virus are very important to understand its pathogenic mechanism, thus leading to the development of antibodies, vaccines and drugs for targeting these proteins and viruses.
SARS-CoV-2 comprised the four structural proteins; the spike (S), nucleocapsid (N), envelope (E) proteins and membrane glycoprotein (M). A complete virus particle (virion) is represented in Figure 1. Cryo-electron microscopy is one of the powerful tools to determine the overall structure of the S protein, thus presenting a unique crown or ‘corona’-like shape.
Three viral proteins; the spike (S), envelope (E) and membrane (M) are embedded in the outer layer of the corona viral particle. The corona viruses protect themselves from the surrounding environment, then the ribonucleic acid (RNA) forms a stable packed in the lipid membrane. The nucleocapsid protein (nucleoprotein) is responsible for tightly wrap the RNA of viruses. However, the fatty membrane of SARS-CoV-2 is sensible to be destroyed by soap, detergent or surfactant.
The nucleocapsid protein significantly involves in viral genomic RNA binding, thus protecting the coiled RNA as its genetic material inside the virus particle. Moreover, the N protein also plays an important role in the early stages of viral infection when the RNA genome is first released into the target host cell.
X-ray crystal structures of the N-terminal (PDB entry 7CDZ) and C-terminal domains have been illustrated here (PDB entry 6WZO). Holo structure of N-terminal domain in complex with double strand RNA (PDB entry 7ACS) has been determined by Nuclear Magnetic Resonance Spectroscopy technique.
The SARS-CoV-2 nucleocapsid protein comprises a total of 419 amino-acid residues as shown in Figure 2a. The N-terminal domain (NTD, residues 49–174) and the C-terminal domain (CTD, residues 247–364) are connected by a flexible linker (residues 175–246) (Figure 2a).
The structure of N-NTD is folded into a right-handed shape and consists of six antiparallel β-sheets (β4-β2-β3-β1-β5-β6), thus forming the palm (Figure 2b). A protruding β-hairpin region locates out of the core subdomain which is formed by a four-stranded antiparallel β-sheet (Figure 2b).
The N-terminal domain of nucleocapsid protein bound to viral RNA forms a ribonucleoprotein complex as shown in Figure 2c. The overall structure of N-NTD complexed with double strand RNA (dsRNA) which is shown in electrostatic surface potential illustrates the negatively charged RNA binding to the positively charged region in the nucleocapsid protein.
The C-terminal domain of nucleocapsid protein forms a cuboid architecture, thus composing of homologous dimers. Each protomer consists of six α-helices and two β-strands (Figure 2d).
Figure 2 (a) Schematic diagram of the nucleocapsid protein (N); the N-terminal domain (NTD and the C-terminal domain (CTD). (b) The overall structure of N-NTD depicted in ribbon representation. (c) The overall structure of N-NTD complexed with dsRNA. (d) The overall structure of C-NTD shown in cartoon representation. Figures were obtained from Yan et al., 2022.
The SARS-CoV-2 N protein is a highly immunogenic viral protein that plays essential roles in corona viral transcription and replication assembly. Moreover, the N protein provides several good advantages: it shares substantial sequence conservation, is less vulnerable to mutation in variants, and activates a stronger protective immune response in the host cells. Therefore, N protein is an excellent potential target for drug design and diagnosis of COVID-19.
Re-written by Chomphunuch Songsiriritthigul (Beamline Scientist, SLRI)
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