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- EMDB-6951: Hepatitis B virus spherical subviral particle -

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Database: EMDB / ID: EMD-6951
TitleHepatitis B virus spherical subviral particle
Map data
SampleHepatitis B virus:
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 30.1 Å
AuthorsCao J / Luo S / Zhang J / Zhu P
CitationJournal: 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.
DepositionApr 29, 2018-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 15, 2019-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: PDBj / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.00597
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00597
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_6951.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
2.5 Å/pix.
x 192 pix.
= 480. Å
2.5 Å/pix.
x 192 pix.
= 480. Å
2.5 Å/pix.
x 192 pix.
= 480. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Contour LevelBy AUTHOR: 0.00597 / Movie #1: 0.00597
Minimum - Maximum-0.033544447 - 0.050881136
Average (Standard dev.)0.00003648378 (±0.003852617)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 480.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z480.000480.000480.000
start NX/NY/NZ-64-64-64
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0340.0510.000

Supplemental data

Sample components

Entire Hepatitis B virus

EntireName: Hepatitis B virus / Number of components: 1

Component #1: virus, Hepatitis B virus

VirusName: Hepatitis B virus / Class: VIRION / Empty: Yes / Enveloped: Yes / Isolate: SEROCOMPLEX
SpeciesSpecies: Hepatitis B virus

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 50 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 5478
3D reconstructionResolution: 30.1 Å / Resolution method: FSC 0.143 CUT-OFF

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