+Open data
-Basic information
Entry | Database: PDB / ID: 7vrn | |||||||||
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Title | Structure of infectious bursal disease virus Gt strain | |||||||||
Components | Structural polyprotein | |||||||||
Keywords | VIRUS / IBDV / icosahedral / attenuated | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / viral capsid / host cell cytoplasm / structural molecule activity / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Avian infectious bursal disease virus (Gumboro virus) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Bao, K.Y. / Zhu, P. | |||||||||
Funding support | China, 2items
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Citation | Journal: Sci Bull (Beijing) / Year: 2022 Title: Cryo-EM structures of infectious bursal disease viruses with different virulences provide insights into their assembly and invasion Authors: Bao, K. / Qi, X. / Lia, Y. / Gong, M. / Wang, M. / Zhu, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vrn.cif.gz | 868 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vrn.ent.gz | 740.6 KB | Display | PDB format |
PDBx/mmJSON format | 7vrn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7vrn_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7vrn_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7vrn_validation.xml.gz | 130.4 KB | Display | |
Data in CIF | 7vrn_validation.cif.gz | 201.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/7vrn ftp://data.pdbj.org/pub/pdb/validation_reports/vr/7vrn | HTTPS FTP |
-Related structure data
Related structure data | 32101MC 7vrpC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 47192.113 Da / Num. of mol.: 13 / Source method: isolated from a natural source Source: (natural) Avian infectious bursal disease virus (Gumboro virus) References: UniProt: Q98VX2, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Infectious bursal disease virus / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Infectious bursal disease virus (Gumboro virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Gallus gallus |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 47.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3917 / Symmetry type: POINT |