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- PDB-7tuk: Small hepatitis B virus surface protein without cytosolic and ant... -

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Basic information

Entry
Database: PDB / ID: 7tuk
TitleSmall hepatitis B virus surface protein without cytosolic and antigenic loops
ComponentsSAg protein
KeywordsVIRAL PROTEIN / HBV / SVP / HBsAg / 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 / membrane / SAg protein
Function and homology information
Biological speciesHBV genotype E (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.3 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

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAg protein
B: SAg protein


Theoretical massNumber of molelcules
Total (without water)50,6082
Polymers50,6082
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 SAg protein


Mass: 25303.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HBV genotype E (virus) / Gene: S / Production host: Homo sapiens (human) / References: UniProt: D6CIG5

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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: HBV genotype E / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: HBV genotype E (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
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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 / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Image recordingAverage exposure time: 3 sec. / Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 36166 / 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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