+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41615 | |||||||||
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Title | The Capsid of Porcine Bocavirus 1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Parvovirus / PBoV1 / Porcine Bocavirus / Capsid / VIRUS | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 2.31 Å | |||||||||
Authors | Velez M / Mietzsch M / McKenna R / Afione S / Zeher A / Huang R / Chiorini J | |||||||||
Funding support | United States, 1 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41615.map.gz | 263 MB | EMDB map data format | |
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Header (meta data) | emd-41615-v30.xml emd-41615.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
Images | emd_41615.png | 277.7 KB | ||
Filedesc metadata | emd-41615.cif.gz | 5.5 KB | ||
Others | emd_41615_half_map_1.map.gz emd_41615_half_map_2.map.gz | 110 MB 109.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41615 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41615 | HTTPS FTP |
-Related structure data
Related structure data | 8tu1MC 8tu0C 8tu2C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41615.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.913 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_41615_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41615_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Porcine bocavirus 1 pig/ZJD/China/2006
Entire | Name: Porcine bocavirus 1 pig/ZJD/China/2006 |
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Components |
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-Supramolecule #1: Porcine bocavirus 1 pig/ZJD/China/2006
Supramolecule | Name: Porcine bocavirus 1 pig/ZJD/China/2006 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 795694 / Sci species name: Porcine bocavirus 1 pig/ZJD/China/2006 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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-Macromolecule #1: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: Porcine bocavirus 1 pig/ZJD/China/2006 |
Molecular weight | Theoretical: 63.370266 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MSSGGDPSED TGAGDGEQGG ESSAMAGRSG GGMGGGGGGG GSVGFSTGGW EGGTYFSDHT VTTTNTRQWY TGILNGHRYS KLAQTTGSN LQAAKPWVGI QTPWAYLNLN CYHCHFSPQD WQRLLNEYKA WRPKRMHVRI YNLQIKQITT VGADTLYQND L TAGVHIFC ...String: MSSGGDPSED TGAGDGEQGG ESSAMAGRSG GGMGGGGGGG GSVGFSTGGW EGGTYFSDHT VTTTNTRQWY TGILNGHRYS KLAQTTGSN LQAAKPWVGI QTPWAYLNLN CYHCHFSPQD WQRLLNEYKA WRPKRMHVRI YNLQIKQITT VGADTLYQND L TAGVHIFC DGSHQYPYAQ HPWDEGASPE LPNEIWKLPQ YAYFQYQGDL TDHATANTPQ NVESMLRSNI PLFLLENSNH EV LRTGEMT EFSFTFQSGW VTNDRAYCCP QSDFNPLVQT RRYYPTWNGS SNSYSYNRYG PYKKPSNWMP GPGLAYKGAT HTN QNPDDA RGPIVTTIAP RGTISVGSTP SNDAPNDGDN TISSDGVKQG GWQTAPVNGA CSRTDYPTLA FDPSDRSTNQ NIPT RNLDI DMTRWYRVHE PVRSGNGSTY YNVDDVWMYP NQVWNSTPIC RDNPIWDKVP RTDHHTLLDS SDGTLPMKHP PGNIF IKCA KIPIPTSNNT DSYLNIYVTG QVTYTVEWEV QRYQTKNWRP ELRTSAGTYN QHEIYNIGEN GTYNRANTFN ECMPTK CGI NRVL UniProtKB: VP2 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.4 µm |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: COMMON LINE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98388 |