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- PDB-7tul: Woodchuck hepatitis small surface protein without cytosolic and a... -

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Basic information

Entry
Database: PDB / ID: 7tul
TitleWoodchuck hepatitis small surface protein without cytosolic and antigenic loops
ComponentsLarge envelope protein
KeywordsVIRAL PROTEIN / WHV / SVP / WHsAg / envelope protein
Function / homologyLarge envelope protein S / Major surface antigen from hepadnavirus / caveolin-mediated endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane / Large envelope protein
Function and homology information
Biological speciesWoodchuck hepatitis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsLiu, H. / Wang, J.C.Y.
Funding support United States, 1items
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 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
B: Large envelope protein
A: Large envelope protein


Theoretical massNumber of molelcules
Total (without water)51,3012
Polymers51,3012
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Large envelope protein / L glycoprotein / L-HBsAg / LHB / Large S protein / Large surface protein / Major surface antigen


Mass: 25650.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Woodchuck hepatitis virus / References: UniProt: P17400

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Woodchuck hepatitis virus 7 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Woodchuck hepatitis virus
Details of virusEmpty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3200 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34520 / Symmetry type: POINT
Atomic model buildingDetails: The authors state that the model was built using 6.5 A cryo-EM map and Alphafold2, so the clashes cannot be totally resolved due to the lack of density from cryo-EM maps.

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