6VYO
Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2
Summary for 6VYO
| Entry DOI | 10.2210/pdb6vyo/pdb |
| Descriptor | Nucleoprotein, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CHLORIDE ION, ... (6 entities in total) |
| Functional Keywords | csgid, covid-19, rna binding domain, nucleocapsid protein, nucleoprotein, structural genomics, center for structural genomics of infectious diseases, viral protein |
| Biological source | Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) |
| Total number of polymer chains | 4 |
| Total formula weight | 57667.32 |
| Authors | Chang, C.,Michalska, K.,Jedrzejczak, R.,Maltseva, N.,Endres, M.,Godzik, A.,Kim, Y.,Joachimiak, A.,Center for Structural Genomics of Infectious Diseases (CSGID) (deposition date: 2020-02-27, release date: 2020-03-11, Last modification date: 2024-02-28) |
| Primary citation | Kim, Y.,Maltseva, N.,Tesar, C.,Jedrzejczak, R.,Endres, M.,Ma, H.,Dugan, H.L.,Stamper, C.T.,Chang, C.,Li, L.,Changrob, S.,Zheng, N.Y.,Huang, M.,Ramanathan, A.,Wilson, P.,Michalska, K.,Joachimiak, A. Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies. Iscience, 27:108976-108976, 2024 Cited by PubMed Abstract: Coronavirus nucleocapsid protein (NP) of SARS-CoV-2 plays a central role in many functions important for virus proliferation including packaging and protecting genomic RNA. The protein shares sequence, structure, and architecture with nucleocapsid proteins from betacoronaviruses. The N-terminal domain (NP) binds RNA and the C-terminal domain is responsible for dimerization. After infection, NP is highly expressed and triggers robust host immune response. The anti-NP antibodies are not protective and not neutralizing but can effectively detect viral proliferation soon after infection. Two structures of SARS-CoV-2 NP were determined providing a continuous model from residue 48 to 173, including RNA binding region and key epitopes. Five structures of NP complexes with human mAbs were isolated using an antigen-bait sorting. Complexes revealed a distinct complement-determining regions and unique sets of epitope recognition. This may assist in the early detection of pathogens and designing peptide-based vaccines. Mutations that significantly increase viral load were mapped on developed, full length NP model, likely impacting interactions with host proteins and viral RNA. PubMed: 38327783DOI: 10.1016/j.isci.2024.108976 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.7 Å) |
Structure validation
Download full validation report
