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Yorodumi- EMDB-1739: Human Bocavirus Capsid structure: Insights into the structural re... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1739 | |||||||||
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Title | Human Bocavirus Capsid structure: Insights into the structural repertoire of the Parvoviridae | |||||||||
Map data | This is a cryo-reconstruction of human bocavirus (HBoV) from virus-like particles of viral protein 2 (VP2) | |||||||||
Sample |
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Keywords | Human Bocavirus / Parvovirus / Virus structure / Electron Cryo-Microscopy / 3D Image Reconstruction / Structural Evolution | |||||||||
Biological species | Human bocavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.9 Å | |||||||||
Authors | Gurda BL / Parent KN / Bladek H / Sinkovits RS / DiMattia MA / Rence C / Castro A / McKenna R / Olson N / Brown K ...Gurda BL / Parent KN / Bladek H / Sinkovits RS / DiMattia MA / Rence C / Castro A / McKenna R / Olson N / Brown K / Baker TS / Agbandje-McKenna M | |||||||||
Citation | Journal: J Virol / Year: 2010 Title: Human bocavirus capsid structure: insights into the structural repertoire of the parvoviridae. Authors: Brittney L Gurda / Kristin N Parent / Heather Bladek / Robert S Sinkovits / Michael A DiMattia / Chelsea Rence / Alejandro Castro / Robert McKenna / Norm Olson / Kevin Brown / Timothy S ...Authors: Brittney L Gurda / Kristin N Parent / Heather Bladek / Robert S Sinkovits / Michael A DiMattia / Chelsea Rence / Alejandro Castro / Robert McKenna / Norm Olson / Kevin Brown / Timothy S Baker / Mavis Agbandje-McKenna / Abstract: Human bocavirus (HBoV) was recently discovered and classified in the Bocavirus genus (family Parvoviridae, subfamily Parvovirinae) on the basis of genomic similarity to bovine parvovirus and canine ...Human bocavirus (HBoV) was recently discovered and classified in the Bocavirus genus (family Parvoviridae, subfamily Parvovirinae) on the basis of genomic similarity to bovine parvovirus and canine minute virus. HBoV has been implicated in respiratory tract infections and gastroenteric disease in children worldwide, yet despite numerous epidemiological reports, there has been limited biochemical and molecular characterization of the virus. Reported here is the three-dimensional structure of recombinant HBoV capsids, assembled from viral protein 2 (VP2), at 7.9-A resolution as determined by cryo-electron microscopy and image reconstruction. A pseudo-atomic model of HBoV VP2 was derived from sequence alignment analysis and knowledge of the crystal structure of human parvovirus B19 (genus Erythrovirus). Comparison of the HBoV capsid structure to that of parvoviruses from five separate genera demonstrates strong conservation of a beta-barrel core domain and an alpha-helix, from which emanate several loops of various lengths and conformations, yielding a unique surface topology that differs from the three already described for this family. The highly conserved core is consistent with observations for other single-stranded DNA viruses, and variable surface loops have been shown to confer the host-specific tropism and the diverse antigenic properties of this family. | |||||||||
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_1739.map.gz | 4.3 MB | EMDB map data format | |
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Header (meta data) | emd-1739-v30.xml emd-1739.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | HBoV.tif | 1.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1739 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1739 | HTTPS FTP |
-Validation report
Summary document | emd_1739_validation.pdf.gz | 208.7 KB | Display | EMDB validaton report |
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Full document | emd_1739_full_validation.pdf.gz | 207.8 KB | Display | |
Data in XML | emd_1739_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1739 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1739 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1739.map.gz / Format: CCP4 / Size: 12.2 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a cryo-reconstruction of human bocavirus (HBoV) from virus-like particles of viral protein 2 (VP2) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.795 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 : Virus-like particles of human Bocavirus viral protein 2
Entire | Name: Virus-like particles of human Bocavirus viral protein 2 |
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Components |
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-Supramolecule #1000: Virus-like particles of human Bocavirus viral protein 2
Supramolecule | Name: Virus-like particles of human Bocavirus viral protein 2 type: sample / ID: 1000 / Oligomeric state: Icosahedral / Number unique components: 1 |
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Molecular weight | Theoretical: 3.66 MDa |
-Supramolecule #1: Human bocavirus
Supramolecule | Name: Human bocavirus / type: virus / ID: 1 / Name.synonym: HBoV / NCBI-ID: 329641 / Sci species name: Human bocavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / Syn species name: HBoV |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
Molecular weight | Theoretical: 3.66 MDa |
Virus shell | Shell ID: 1 / Name: Viral protein 2 / Diameter: 280 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 | 10 mg/mL |
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Buffer | pH: 7.5 / Details: 20 mM Tris-HCl, 150 mM NaCl, 2 mM MgCl2 |
Grid | Details: Quantifoil grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 89 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Manual plunge-freezer / Method: Blot for 5 sec before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Min: 90 K / Max: 90 K / Average: 90 K |
Alignment procedure | Legacy - Astigmatism: Corrected at 39,000 x magnification with FFT |
Date | Apr 22, 2008 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 1.795 µm / Number real images: 16 / Average electron dose: 9 e/Å2 / Od range: 1.5 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.25 µm / Nominal defocus min: 0.95 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: Polara Multi Specimen Holder / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: ROBEM |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 3754 |