+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6951 | |||||||||
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Title | Hepatitis B virus spherical subviral particle | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Hepatitis B virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 30.1 Å | |||||||||
Authors | Cao J / Luo S / Zhang J / Zhu P | |||||||||
Citation | Journal: Virus Res / Year: 2019 Title: Cryo-EM structure of native spherical subviral particles isolated from HBV carriers. Authors: Jianhao Cao / Junchang Zhang / Yanmeng Lu / Shuhong Luo / Jingqiang Zhang / Ping Zhu / Abstract: Hepatitis B virus (HBV) contains 3 types of particles, i.e., 22-nm-diameter spherical and tubular subviral particles (SVPs) and 44-nm-diameter Dane particles. The SVPs are non-infectious and present ...Hepatitis B virus (HBV) contains 3 types of particles, i.e., 22-nm-diameter spherical and tubular subviral particles (SVPs) and 44-nm-diameter Dane particles. The SVPs are non-infectious and present strong immunogenicity, while Dane particles are infectious. In this study, we isolated spherical SVPs from HBV carriers' sera and determined their 3D structure at the resolution of ∼30 Å by cryo-electron microscopy (cryo-EM) single-particle reconstruction. Our cryo-EM structure suggests that the native HBV spherical SVP is irregularly organized, where spike-like features are arranged in a crystalline-like pattern on the surface. Strikingly, the hepatitis B surface antigen (HBsAg) in the native spherical SVPs folds as protrusions on the surface, as those on the native tubular SVPs and Dane particles, but is largely different from that in the recombinant octahedral SVPs. These results suggest a universal folding shape of HBsAg on the native HBV viral and subviral particles. | |||||||||
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_6951.map.gz | 20.7 MB | EMDB map data format | |
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Header (meta data) | emd-6951-v30.xml emd-6951.xml | 7.2 KB 7.2 KB | Display Display | EMDB header |
Images | emd_6951.png | 75.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6951 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6951 | HTTPS FTP |
-Validation report
Summary document | emd_6951_validation.pdf.gz | 78 KB | Display | EMDB validaton report |
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Full document | emd_6951_full_validation.pdf.gz | 77.1 KB | Display | |
Data in XML | emd_6951_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6951 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6951 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6951.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 2.5 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 : Hepatitis B virus
Entire | Name: Hepatitis B virus |
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Components |
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-Supramolecule #1: Hepatitis B virus
Supramolecule | Name: Hepatitis B virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Virus type: VIRION / Virus isolate: SEROCOMPLEX / Virus enveloped: Yes / Virus empty: Yes |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Sugar embedding | Material: ice |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 30.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5478 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: PROJECTION MATCHING |