Nucleocapsid Protein of Coronavirus
The coronavirus nucleocapsid protein (N protein) is a structural protein that forms complexes with genomic RNA, interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly.
Amino acid sequence comparisons have shown that CoV N proteins have three distinct and highly conserved domains: two structural and independently folded structural regions, namely the N terminal domain (NTD/domain 1) and C-terminal domain (CTD/domain 3), which are separated by a intrinsically disordered central region (RNA-binding domain/domain 2); all three domains have been shown in different CoVs to bind with viral RNA.
There are several common characteristics of CoV N protein NTDs, including predicted secondary structures such as a central β-sheet platform flanked by α-helices, with a basic RNA binding groove along the β-platform and an extended β-hairpin. The NTD is enriched in aromatic and basic residues and the folded shape resembles a hand with basic fingers that extend far beyond the protein core, a hydrophobic palm, and an acidic―wrist. It has been proposed that the flexible, positively charged finger-like β-hairpin extension in the NTD of both IBV and SARS-CoV N protein is able to grasp RNA by neutralizing its phosphate groups, while the base moieties can make contact with exposed aromatic residues from the hydrophobic palm.
The NTD is separated from the CTD by an intrinsically disordered middle region referred to as the linker region (LKR). The charged LKR is also known as the SR-domain because it is rich in serine and arginine residues, and it is involved in cell signaling. The flexible LKR is capable of direct interaction with RNA under in vitro conditions.Potential phosphorylation sites have been mapped to the Ser/Arg-rich portion of the LKR of SARS-CoV N. These LKR phosphorylation sites are thought to function in binding M protein, heteronuclear ribonucleoprotein (hnRNP-A1) and RNA to the N protein with high binding affinity.
Domain organization of the Severe Acute Respiratory Syndrome human coronavirus (SARS-CoV) nucleocapsid protein. IDR (a.a. 1–44; 182–247; 366–422)—intrinsically disordered regions; NTD (a.a. 45–181)—N terminal domain; LKR (182–247)—linker region; CTD (248–365)—C-terminal domain. The charged SR rich (striated box) and the nuclear localization signal (NLS, solid box) motifs are shown.
The CTD, which is a hydrophobic, helix-rich terminal, has been mapped for SARS-N to aa 248–365. This domain is also referred to as the dimerization domain because it contains residues responsible for self-association to form homodimers, as well as homo-oligomers through a domain-swapping mechanism. Oligomerization of N protein is necessary to produce a stable conformation because in its monomeric form, the CTD folds into an extended conformation with a large cavity in its center, making it unstable. Sequence comparison shows that the dimerization domain of the N protein is conserved at least among the alpha, beta and gamma groups of CoVs, suggesting a common structural and functional role for this domain.
The coronavirus N protein is abundantly produced within infected cells. N protein has multiple functions, including binding to viral RNA to form the ribonucleocapsid and has also been proposed to have roles in virus replication, transcription and translation. In host cells, N proteins have been shown to cause deregulation of the cell-cycle, inhibit the production of interferon, up-regulate the production of COX2, up-regulate the activity of AP1,and induce apoptosis in serum deprived cells—of all which may have possible pathological consequences.
|1. Virus Life Cycle||Function|
|1.1. Viral Core Formation||
Primary role of CoV N is packaging the viral genome into long, flexible, helical RNP complexes.
|1.2. Viral Assembly||
CoV N protein dimerization and association with viral genomic RNA is critical for viral assembly.
Interaction amongst the viral structural proteins (N, E, S and M), as well as a host membrane envelope obtained from the site of budding is required for viral assembly.
|1.3. Virus Budding/envelope formation||
Association of CoV N with the ER-Golgi complex plays a role in virus budding.
Presence of N results in increased yields of VLPs and complete virion formation.
|1.4. Genomic mRNA replication/genomic RNA synthesis||
Intracellular co-localization of N with replicase components is required for RNA synthesis.
Translation of N protein is implicated in stimulation of gRNA infection during RNA synthesis.
|2. Cellular Response|
|2.1. Chaperone activity||
All CoV N proteins involved in proper folding of nucleic acids by RNA chaperone proteins.
|2.2. Cell cycle regulation||
SARS-CoV N modulates the host cell cycle by regulating cyclin-CDKactivity. Leads to the arrest in progression of S phase.
|2.3. Cell stress responses—host translational shutoff||
SARS-N and MHV-N interact with cellular hnRNP-A1, which could act as a switch that redirects viral activity from RNA synthesis to nucleocapsid formation.
Interaction of N protein CTD with elongation factor 1α (EF1α), a major translational factor in mammalian cells, can suppress translation.
|2.4. Viral pathogenesis—Immune system interference||
N protein plays an important role in viral pathogenesis. Mice infected with JMHV protected by anti-N monoclonal antibodies.
Synthesis of type-1 interferon (1FN) inhibited by SARS-CoV N.
The CTD of N has been shown to be a critical antagonist of 1FN induction.
|2.5. Signal transduction||
Activation of host cell signal transduction pathways and kinases leads to phosphorylation of N.
|PKSR030486||Recombinant 2019-nCoV NP NTD domain (His Tag)||/||N-His||E.coli||/|
|PKSR030487||Recombinant 2019-nCoV NP CTD domain Protein||/||/||E.coli||/|
|PKSR030485||Recombinant 2019-nCoV Nucleocapsid Protein (His Tag)||Met1-Ala419||N-His||E.coli||/|
|PKSR030497||Recombinant 2019-nCoV Nucleocapsid Protein (His Tag)||Met1-Ala419||C-His||Baculovirus-Insect Cells||/|
|PKSR030512||Recombinant 2019-nCoV Nucleocapsid Protein, Biotinylated (His Tag)||(Met1-Ala419(335Gly/Ala))||C-His||Baculovirus-Insect Cells||/|
|E-AB-V1011||SARS-COV-2 NP Monoclonal Antibody(2019-nCoV)||Mouse / Human||IgG1||ELISA|
|E-AB-V1012||SARS-COV-2 NP ScFv Monoclonal Antibody(2019-nCoV)||Mouse / Human||IgG1||ELISA|
|E-AB-V1013||SARS-COV-2 NP Monoclonal Antibody(2019-nCoV)||Mouse||IgG1||WB,ELISA|
|E-AB-V1014||SARS-COV-2 NP Monoclonal Antibody(2019-nCoV)||Rabbit||IgG||WB,ELISA|
|E-AB-V1015||SARS-COV-2 NP Polyclonal Antibody(2019-nCoV)||Rabbit||IgG||WB,ELISA|
|E-AB-V1016||SARS-COV-2 NP Polyclonal Antibody(2019-nCoV)||Rabbit||IgG||ELISA|
- 1.Laude, H.; Masters, P. The coronavirus nucleocapsid protein. In Coronaviruses and Arteriviruses; Plenum Press: New York, NY, USA,1995; pp. 141–163.
- 2.McBride R, Van Zyl M, Fielding B C. The coronavirus nucleocapsid is a multifunctional protein[J]. Viruses, 2014, 6(8): 2991-3018.3. Jayaram, H.; Fan, H.; Bowman, B.R.; et al. X-ray structures of the N-and C-terminal domains of a coronavirus nucleocapsid protein: Implications for nucleocapsid formation. J. Virol.2006,80, 6612–6620.
- 3.Jayaram, H.; Fan, H.; Bowman, B.R.; Ooi, A.; Jayaram, J.; Collisson, E.W.; Lescar, J.; Prasad, B.V.X-ray structures of the N-and C-terminal domains of a coronavirus nucleocapsid protein: Implications for nucleocapsid formation. J. Virol.2006,80, 6612–6620.
- 4.Fan, H.; Ooi, A.; Tan, Y.W.; et al. The nucleocapsid protein of coronavirus infectious bronchitis virus: Crystal structure of its N-terminal domain and multimerization properties. Structure 2005,13, 1859–1868.
- 5.Hurst, K.R.; Koetzner, C.A.; Masters, P.S. Identification of in vivo-interacting domains of the murine coronavirus nucleocapsid protein. J. Virol.2009,83, 7221–7234.
- 6.Parker, M.M.; Masters, P.S. Sequence comparison of the N genes of five strains of the coronavirus mouse hepatitis virus suggests a three domain structure for the nucleocapsid protein.Virology 1990, 179, 463–468.
- 7.Chang, C.K.; Hsu, Y.L.; Chang, Y.H.; et al. Multiple nucleic acid binding sites and intrinsic disorder of severe acute respiratory syndrome coronavirus nucleocapsid protein: Implications for ribonucleocapsid protein packaging. J. Virol.2009, 83, 2255–2264.
- 8.Peng, T.Y.; Lee, K.R.; Tarn, W.Y. Phosphorylation of the arginine/serine dipeptide-rich motif of the severe acute respiratory syndrome coronavirus nucleocapsid protein modulates its multimerization, translation inhibitory activity and cellular localization. FEBS J. 2008, 275,4152–4163.
- 9.Masters, P. Localization of an RNA-binding domain in the nucleocapsid protein of the coronavirus mouse hepatitis virus. Arch. Virol. 1992, 125, 141–160.
- 10.Chang, C.K.; Sue, S.C.; Yu, T.H.; et al. The dimer interface of the SARS coronavirus nucleocapsid protein adapts a porcine respiratory and reproductive syndrome virus-like structure. FEBS Lett. 2005,579, 5663–5668.
- 11.Yu, I.M.; Oldham, M.L.; Zhang, J.; Chen, J. Crystal structure of the severe acute respiratorysyndrome (SARS) coronavirus nucleocapsid protein dimerization domain reveals evolutionarylinkage between corona- and arteriviridae. J. Biol. Chem. 2006, 281, 17134–17139.