+Open data
-Basic information
Entry | Database: PDB / ID: 8tu1 | ||||||
---|---|---|---|---|---|---|---|
Title | The Capsid of Porcine Bocavirus 1 | ||||||
Components | VP2 | ||||||
Keywords | VIRUS / Parvovirus / PBoV1 / Porcine Bocavirus / Capsid | ||||||
Function / homology | Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / T=1 icosahedral viral capsid / structural molecule activity / VP2 Function and homology information | ||||||
Biological species | Porcine bocavirus 1 pig/ZJD/China/2006 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.31 Å | ||||||
Authors | Velez, M. / Mietzsch, M. / McKenna, R. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Viruses / Year: 2023 Title: Structural Characterization of Canine Minute Virus, Rat and Porcine Bocavirus. Authors: Michael Velez / Mario Mietzsch / Jane Hsi / Logan Bell / Paul Chipman / Xiaofeng Fu / Robert McKenna / Abstract: is an expansive genus of the , with a wide range of vertebrate hosts. This study investigates Canine minute virus (CnMV), Rat bocavirus (RBoV), and Porcine bocavirus 1 (PBoV1). Both CnMV and PBoV1 ... is an expansive genus of the , with a wide range of vertebrate hosts. This study investigates Canine minute virus (CnMV), Rat bocavirus (RBoV), and Porcine bocavirus 1 (PBoV1). Both CnMV and PBoV1 have been found in gastrointestinal infections in their respective hosts, with CnMV responsible for spontaneous abortions in dogs, while PBoV has been associated with encephalomyelitis in piglets. The pathogenicity of the recently identified RBoV is currently unknown. To initiate the characterization of these viruses, their capsids structures were determined by cryo-electron microscopy at resolutions ranging from 2.3 to 2.7 Å. Compared to other parvoviruses, the CnMV, PBoV1, and RBoV capsids showed conserved features, such as the channel at the fivefold symmetry axis. However, major differences were observed at the two- and threefold axes. While CnMV displays prominent threefold protrusions, the same region is more recessed in PBoV1 and RBoV. Furthermore, the typical twofold axis depression of parvoviral capsids is absent in CnMV or very small in PBoV and RBoV. These capsid structures extend the structural portfolio for the genus and will allow future characterization of these pathogens on a molecular level. This is important, as no antivirals or vaccines exist for these viruses. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8tu1.cif.gz | 5.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8tu1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8tu1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8tu1_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8tu1_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8tu1_validation.xml.gz | 323 KB | Display | |
Data in CIF | 8tu1_validation.cif.gz | 494.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/8tu1 ftp://data.pdbj.org/pub/pdb/validation_reports/tu/8tu1 | HTTPS FTP |
-Related structure data
Related structure data | 41615MC 8tu0C 8tu2C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 63370.266 Da / Num. of mol.: 60 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine bocavirus 1 pig/ZJD/China/2006 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: D7RF54 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Porcine bocavirus 1 pig/ZJD/China/2006 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Porcine bocavirus 1 pig/ZJD/China/2006 |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9 |
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 7.4 |
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 |
---|---|
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 / Nominal defocus max: 3000 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98388 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|