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Yorodumi- PDB-3jbm: Electron cryo-microscopy of a virus-like particle of orange-spott... -
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-Basic information
Entry | Database: PDB / ID: 3jbm | ||||||
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Title | Electron cryo-microscopy of a virus-like particle of orange-spotted grouper nervous necrosis virus | ||||||
Components | virus-like particle of orange-spotted grouper nervous necrosis virus | ||||||
Keywords | VIRUS / virus-like particle / orange-spotted grouper nervous necrosis virus / betanodavirus | ||||||
Function / homology | Nodavirus capsid / nodavirus capsid protein / Viral coat protein subunit / Virus-like particle of orange-spotted grouper nervous necrosis virus Function and homology information | ||||||
Biological species | Orange-spotted grouper nervous necrosis virus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Xie, J. / Li, K. / Gao, Y. / Huang, R. / Lai, Y. / Shi, Y. / Yang, S. / Zhu, G. / Zhang, Q. / He, J. | ||||||
Citation | Journal: Vet Res / Year: 2016 Title: Structural analysis and insertion study reveal the ideal sites for surface displaying foreign peptides on a betanodavirus-like particle. Authors: Junfeng Xie / Kunpeng Li / Yuanzhu Gao / Runqing Huang / Yuxiong Lai / Yan Shi / Shaowei Yang / Guohua Zhu / Qinfen Zhang / Jianguo He / Abstract: Betanodavirus infection causes fatal disease of viral nervous necrosis in many cultured marine and freshwater fish worldwide and the virus-like particles (VLP) are effective vaccines against ...Betanodavirus infection causes fatal disease of viral nervous necrosis in many cultured marine and freshwater fish worldwide and the virus-like particles (VLP) are effective vaccines against betanodavirus. But vaccine and viral vector designs of betanodavirus VLP based on their structures remain lacking. Here, the three-dimensional structure of orange-spotted grouper nervous necrosis virus (OGNNV) VLP (RBS) at 3.9 Å reveals the organization of capsid proteins (CP). Based on the structural results, seven putative important sites were selected to genetically insert a 6× histidine (His)-tag for VLP formation screen, resulting in four His-tagged VLP (HV) at positions N-terminus, Ala220, Pro292 and C-terminus. The His-tags of N-terminal HV (NHV) were concealed inside virions while those of 220HV and C-terminal HV (CHV) were displayed at the outer surface. NHV, 220HV and CHV maintained the same cell entry ability as RBS in the Asian sea bass (SB) cell line, indicating that their similar surface structures can be recognized by the cellular entry receptor(s). For application of vaccine design, chromatography-purified CHV could provoke NNV-specific antibody responses as strong as those of RBS in a sea bass immunization assay. Furthermore, in carrying capacity assays, N-terminus and Ala220 can only carry short peptides and C-terminus can even accommodate large protein such as GFP to generate fluorescent VLP (CGV). For application of a viral vector, CGV could be real-time visualized to enter SB cells in invasion study. All the results confirmed that the C-terminus of CP is a suitable site to accommodate foreign peptides for vaccine design and viral vector development. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 3jbm.cif.gz | 38.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jbm.ent.gz | 22.1 KB | Display | PDB format |
PDBx/mmJSON format | 3jbm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jbm_validation.pdf.gz | 984.9 KB | Display | wwPDB validaton report |
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Full document | 3jbm_full_validation.pdf.gz | 987.1 KB | Display | |
Data in XML | 3jbm_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | 3jbm_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/3jbm ftp://data.pdbj.org/pub/pdb/validation_reports/jb/3jbm | HTTPS FTP |
-Related structure data
Related structure data | 6453MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
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-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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