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- EMDB-26119: Woodchuck hepatitis B virus small spherical subviral particle tre... -

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Basic information

Entry
Database: EMDB / ID: EMD-26119
TitleWoodchuck hepatitis B virus small spherical subviral particle treated with 0.1% NP-40
Map dataHepatitis B virus small spherical subviral particle treated with 0.1% NP-40
Sample
  • Virus: Woodchuck hepatitis virus 7
KeywordsWHV / SVP / spherical / WHs / NP40 / VIRAL PROTEIN
Biological speciesWoodchuck hepatitis virus 7
Methodsingle particle reconstruction / cryo EM / Resolution: 9.7 Å
AuthorsLiu H / Wang JCY
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Sci Adv / Year: 2022
Title: Cryo-EM structures of human hepatitis B and woodchuck hepatitis virus small spherical subviral particles.
Authors: Haitao Liu / Xupeng Hong / Ji Xi / Stephan Menne / Jianming Hu / Joseph Che-Yen Wang /
Abstract: The loss of detectable hepatitis B surface antigen (HBsAg) is considered a functional cure in chronic hepatitis B. Naturally, HBsAg can be incorporated into the virion envelope or assembled into ...The loss of detectable hepatitis B surface antigen (HBsAg) is considered a functional cure in chronic hepatitis B. Naturally, HBsAg can be incorporated into the virion envelope or assembled into subviral particles (SVPs) with lipid from host cells. Until now, there has been no detailed structure of HBsAg, and the published SVP structures are controversial. Here, we report the first subnanometer-resolution structures of spherical SVP from hepatitis B virus (HBV) and the related woodchuck hepatitis virus (WHV) determined by cryo-electron microscopy in combination with AlphaFold2 prediction. Both structures showed unique rhombicuboctahedral symmetry with 24 protruding spikes comprising dimer of small HBsAg with four helical domains. The lipid moiety in the SVP is organized in a noncanonical lipid patch instead of a lipid bilayer, which can accommodate the exposed hydrophobic surface and modulate particle stability. Together, these findings advance our knowledge of viral membrane organization and the structures of HBV and WHV spherical SVPs.
History
DepositionFeb 1, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26119.png

Downloads & links

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Map

FileDownload / File: emd_26119.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHepatitis B virus small spherical subviral particle treated with 0.1% NP-40
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 280 pix.
= 379.68 Å		1.36 Å/pix.
x 280 pix.
= 379.68 Å		1.36 Å/pix.
x 280 pix.
= 379.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.356 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00713
Minimum - Maximum-0.010751752 - 0.01756286
Average (Standard dev.)0.000047350455 (±0.0014521704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 379.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Woodchuck hepatitis virus 7

EntireName: Woodchuck hepatitis virus 7
Components
  • Virus: Woodchuck hepatitis virus 7

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Supramolecule #1: Woodchuck hepatitis virus 7

SupramoleculeName: Woodchuck hepatitis virus 7 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10432 / Sci species name: Woodchuck hepatitis virus 7 / Virus type: VIRION / Virus isolate: STRAIN / 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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
DetailsCsCl fraction samples treated with NP40 after dialyze

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / Average exposure time: 3.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 8409
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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