+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6168 | |||||||||
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Title | Structure of Enteric Pathogen Bovine Parvovirus | |||||||||
Map data | Reconstruction of Bovine Parvovirus VP2 capsid | |||||||||
Sample |
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Keywords | BPV / parvovirus / bocavirus capsid / vp2 | |||||||||
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 / Capsid protein VP2 / VP2 Function and homology information | |||||||||
Biological species | Bovine parvovirus-1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.8 Å | |||||||||
Authors | Kailasan S / Halder S / Gurda B / Bladek H / Chipman PR / McKenna R / Brown K / Agbandje-McKenna M | |||||||||
Citation | Journal: J Virol / Year: 2015 Title: Structure of an enteric pathogen, bovine parvovirus. Authors: Shweta Kailasan / Sujata Halder / Brittney Gurda / Heather Bladek / Paul R Chipman / Robert McKenna / Kevin Brown / Mavis Agbandje-McKenna / Abstract: Bovine parvovirus (BPV), the causative agent of respiratory and gastrointestinal disease in cows, is the type member of the Bocaparvovirus genus of the Parvoviridae family. Toward efforts to obtain a ...Bovine parvovirus (BPV), the causative agent of respiratory and gastrointestinal disease in cows, is the type member of the Bocaparvovirus genus of the Parvoviridae family. Toward efforts to obtain a template for the development of vaccines and small-molecule inhibitors for this pathogen, the structure of the BPV capsid, assembled from the major capsid viral protein 2 (VP2), was determined using X-ray crystallography as well as cryo-electron microscopy and three-dimensional image reconstruction (cryo-reconstruction) to 3.2- and 8.8-Å resolutions, respectively. The VP2 region ordered in the crystal structure, from residues 39 to 536, conserves the parvoviral eight-stranded jellyroll motif and an αA helix. The BPV capsid displays common parvovirus features: a channel at and depressions surrounding the 5-fold axes and protrusions surrounding the 3-fold axes. However, rather than a depression centered at the 2-fold axes, a raised surface loop divides this feature in BPV. Additional observed density in the capsid interior in the cryo-reconstructed map, compared to the crystal structure, is interpreted as 10 additional N-terminal residues, residues 29 to 38, that radially extend the channel under the 5-fold axis, as observed for human bocavirus 1 (HBoV1). Surface loops of various lengths and conformations extend from the core jellyroll motif of VP2. These loops confer the unique surface topology of the BPV capsid, making it strikingly different from HBoV1 as well as the type members of other Parvovirinae genera for which structures have been determined. For the type members, regions structurally analogous to those decorating the BPV capsid surface serve as determinants of receptor recognition, tissue and host tropism, pathogenicity, and antigenicity. IMPORTANCE: Bovine parvovirus (BPV), identified in the 1960s in diarrheic calves, is the type member of the Bocaparvovirus genus of the nonenveloped, single-stranded DNA (ssDNA) Parvoviridae family. ...IMPORTANCE: Bovine parvovirus (BPV), identified in the 1960s in diarrheic calves, is the type member of the Bocaparvovirus genus of the nonenveloped, single-stranded DNA (ssDNA) Parvoviridae family. The recent isolation of human bocaparvoviruses from children with severe respiratory and gastrointestinal infections has generated interest in understanding the life cycle and pathogenesis of these emerging viruses. We have determined the high-resolution structure of the BPV capsid assembled from its predominant capsid protein VP2, known to be involved in a myriad of functions during host cell entry, pathogenesis, and antigenicity for other members of the Parvovirinae. Our results show the conservation of the core secondary structural elements and the location of the N-terminal residues for the known bocaparvovirus capsid structures. However, surface loops with high variability in sequence and conformation give BPV a unique capsid surface topology. Similar analogous regions in other Parvovirinae type members are important as determinants of receptor recognition, tissue and host tropism, pathogenicity, and antigenicity. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6168.map.gz | 4.6 MB | EMDB map data format | |
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Header (meta data) | emd-6168-v30.xml emd-6168.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | emd_6168.tif | 1.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6168 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6168 | HTTPS FTP |
-Validation report
Summary document | emd_6168_validation.pdf.gz | 78.2 KB | Display | EMDB validaton report |
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Full document | emd_6168_full_validation.pdf.gz | 77.3 KB | Display | |
Data in XML | emd_6168_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6168 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6168 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6168.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Bovine Parvovirus VP2 capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Bovine Parvovirus VP2 Virus-like particle
Entire | Name: Bovine Parvovirus VP2 Virus-like particle |
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Components |
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-Supramolecule #1000: Bovine Parvovirus VP2 Virus-like particle
Supramolecule | Name: Bovine Parvovirus VP2 Virus-like particle / type: sample / ID: 1000 / Oligomeric state: 60mer / Number unique components: 1 |
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Molecular weight | Experimental: 3.6 MDa / Theoretical: 3.6 MDa / Method: SDS PAGE, Mass Spectrometry |
-Supramolecule #1: Bovine parvovirus-1
Supramolecule | Name: Bovine parvovirus-1 / type: virus / ID: 1 / NCBI-ID: 365609 / Sci species name: Bovine parvovirus-1 / Sci species strain: Haden / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Bos taurus (cattle) / synonym: VERTEBRATES |
Host system | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 / Recombinant plasmid: pFastbac-1 |
Molecular weight | Experimental: 3.6 MDa / Theoretical: 3.6 MDa |
Virus shell | Shell ID: 1 / Name: VP2 / Diameter: 275 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8.0 mg/mL |
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Buffer | pH: 7.4 / Details: Tris-HCl |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 92,000 times magnification. |
Date | Feb 5, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 63 / Average electron dose: 20 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 67047 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.98 µm / Nominal defocus min: 1.26 µm / Nominal magnification: 67047 |
Sample stage | Specimen holder: 626 / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Details | Manual selection in Robem |
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CTF correction | Details: each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: OTHER / Software - Name: Auto3DEM / Number images used: 1131 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient |