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- PDB-7tul: Woodchuck hepatitis small surface protein without cytosolic and a... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tul | ||||||
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Title | Woodchuck hepatitis small surface protein without cytosolic and antigenic loops | ||||||
![]() | Large envelope protein | ||||||
![]() | VIRAL PROTEIN / WHV / SVP / WHsAg / envelope protein | ||||||
Function / homology | Large envelope protein S / Major surface antigen from hepadnavirus / caveolin-mediated endocytosis of virus by host cell / membrane => GO:0016020 / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / Large envelope protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 Å | ||||||
![]() | Liu, H. / Wang, J.C.Y. | ||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.7 KB | Display | ![]() |
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PDB format | ![]() | 86.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 871.5 KB | Display | ![]() |
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Full document | ![]() | 884 KB | Display | |
Data in XML | ![]() | 21 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 26118MC ![]() 7tukC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 25650.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Woodchuck hepatitis virus 7 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Details of virus | Empty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRION |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3200 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34520 / Symmetry type: POINT |
Atomic model building | Details: 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. |