Structural basis of a human antibody targeting SARS-CoV-2 nucleocapsid protein dimerization domain and interfering with RNA-binding
Abstract The transition of SARS-CoV-2 into a recurrent, seasonal pathogen has underscored the need for the induction of durable immune protection. The nucleocapsid (N) protein is regarded as a promising complementary target for therapeutic and vaccine strategies, owing to its structural robustness,...
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Nature Portfolio
2025-08-01
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| Series: | Communications Biology |
| Online Access: | https://doi.org/10.1038/s42003-025-08648-x |
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| author | Shaojie Xue Suhua He Zhaoxia Huang Mei Yang Guowei Hu Xiaoxue Chen Qiuyue Chen Wenying Zhou Sixiao Lin Shoudeng Chen |
| author_facet | Shaojie Xue Suhua He Zhaoxia Huang Mei Yang Guowei Hu Xiaoxue Chen Qiuyue Chen Wenying Zhou Sixiao Lin Shoudeng Chen |
| author_sort | Shaojie Xue |
| collection | DOAJ |
| description | Abstract The transition of SARS-CoV-2 into a recurrent, seasonal pathogen has underscored the need for the induction of durable immune protection. The nucleocapsid (N) protein is regarded as a promising complementary target for therapeutic and vaccine strategies, owing to its structural robustness, clinical relevance, and ability to elicit critical immune response. Within the N protein, the C-terminal domain (N-CTD) plays a pivotal role in assembly of viral RNA (vRNA)-N protein complexes, and in facilitating liquid-liquid phase separation (LLPS) through specific interactions with RNA on its dimerization surface. Despite its functional importance, the molecular mechanisms by which the RNA-binding surface of this domain can be selectively targeted by inhibitors remain poorly defined. Herein, we report a 2.06 Å crystal structure of the SARS-CoV-2 N-CTD in complex with nCoV400Fab, a human monoclonal antibody derived from single B-cell screening. The structure reveals that nCoV400Fab engages multiple basic residues on the RNA-binding surface, forming a steric blockade that hinders vRNA binding. Functional assays demonstrate that nCoV400Fab disrupts both viral ribonucleoprotein (vRNP) assembly and RNA-induced condensate formation. Together, these findings define a structural mechanism by which a human antibody disrupts the RNA-binding surface of N-CTD, laying the foundation for the development of macromolecular inhibitors. |
| format | Article |
| id | doaj-art-6d727c51ec4548beade8af4a234aa5c2 |
| institution | Kabale University |
| issn | 2399-3642 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Communications Biology |
| spelling | doaj-art-6d727c51ec4548beade8af4a234aa5c22025-08-24T11:45:52ZengNature PortfolioCommunications Biology2399-36422025-08-018111310.1038/s42003-025-08648-xStructural basis of a human antibody targeting SARS-CoV-2 nucleocapsid protein dimerization domain and interfering with RNA-bindingShaojie Xue0Suhua He1Zhaoxia Huang2Mei Yang3Guowei Hu4Xiaoxue Chen5Qiuyue Chen6Wenying Zhou7Sixiao Lin8Shoudeng Chen9Molecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen UniversityGuangzhou National LaboratoryMolecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen UniversityMolecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen UniversityMolecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen UniversityDepartment of Pharmacy, Sun-Yat-Sen Memorial Hospital, Sun Yat-sen UniversityDepartment of Radiology, The Fifth Affiliated Hospital of Sun Yat-sen UniversityCentral Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen UniversityCentral Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen UniversityMolecular Imaging Center, The Fifth Affiliated Hospital, Sun Yat-sen UniversityAbstract The transition of SARS-CoV-2 into a recurrent, seasonal pathogen has underscored the need for the induction of durable immune protection. The nucleocapsid (N) protein is regarded as a promising complementary target for therapeutic and vaccine strategies, owing to its structural robustness, clinical relevance, and ability to elicit critical immune response. Within the N protein, the C-terminal domain (N-CTD) plays a pivotal role in assembly of viral RNA (vRNA)-N protein complexes, and in facilitating liquid-liquid phase separation (LLPS) through specific interactions with RNA on its dimerization surface. Despite its functional importance, the molecular mechanisms by which the RNA-binding surface of this domain can be selectively targeted by inhibitors remain poorly defined. Herein, we report a 2.06 Å crystal structure of the SARS-CoV-2 N-CTD in complex with nCoV400Fab, a human monoclonal antibody derived from single B-cell screening. The structure reveals that nCoV400Fab engages multiple basic residues on the RNA-binding surface, forming a steric blockade that hinders vRNA binding. Functional assays demonstrate that nCoV400Fab disrupts both viral ribonucleoprotein (vRNP) assembly and RNA-induced condensate formation. Together, these findings define a structural mechanism by which a human antibody disrupts the RNA-binding surface of N-CTD, laying the foundation for the development of macromolecular inhibitors.https://doi.org/10.1038/s42003-025-08648-x |
| spellingShingle | Shaojie Xue Suhua He Zhaoxia Huang Mei Yang Guowei Hu Xiaoxue Chen Qiuyue Chen Wenying Zhou Sixiao Lin Shoudeng Chen Structural basis of a human antibody targeting SARS-CoV-2 nucleocapsid protein dimerization domain and interfering with RNA-binding Communications Biology |
| title | Structural basis of a human antibody targeting SARS-CoV-2 nucleocapsid protein dimerization domain and interfering with RNA-binding |
| title_full | Structural basis of a human antibody targeting SARS-CoV-2 nucleocapsid protein dimerization domain and interfering with RNA-binding |
| title_fullStr | Structural basis of a human antibody targeting SARS-CoV-2 nucleocapsid protein dimerization domain and interfering with RNA-binding |
| title_full_unstemmed | Structural basis of a human antibody targeting SARS-CoV-2 nucleocapsid protein dimerization domain and interfering with RNA-binding |
| title_short | Structural basis of a human antibody targeting SARS-CoV-2 nucleocapsid protein dimerization domain and interfering with RNA-binding |
| title_sort | structural basis of a human antibody targeting sars cov 2 nucleocapsid protein dimerization domain and interfering with rna binding |
| url | https://doi.org/10.1038/s42003-025-08648-x |
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