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

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Basic information

Entry
Database: EMDB / ID: EMD-6951
TitleHepatitis B virus spherical subviral particle
Map data
Sample
  • Virus: Hepatitis 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.
History
DepositionApr 29, 2018-
Header (metadata) releaseMay 15, 2019-
Map releaseMay 15, 2019-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • 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:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6951.png

Downloads & links

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Map

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

Image control

Size
Brightness
Contrast
Others
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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density

Histogram

Histogram (log scale)
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
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
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
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0340.0510.000

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Supplemental data

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Sample components

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Entire : Hepatitis B virus

EntireName: Hepatitis B virus
Components
  • Virus: Hepatitis B virus

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Supramolecule #1: Hepatitis B virus

SupramoleculeName: 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

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Sugar embeddingMaterial: ice
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 30.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5478
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING

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