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- EMDB-61003: Structure of HBV surface antigen determined in recombinant spheri... -

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Basic information

Entry
Database: EMDB / ID: EMD-61003
TitleStructure of HBV surface antigen determined in recombinant spherical subviral particle
Map datasharpened map
Sample
  • Complex: HBV surface antigen dimer
    • Protein or peptide: Large envelope protein
  • Ligand: ZINC ION
KeywordsHBV / HBsAg / VIRAL 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 / virion attachment to host cell / virion membrane / membrane / Large envelope protein
Function and homology information
Biological speciesHBV genotype D3 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChen L / He X
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31821091 China
CitationJournal: Cell Discov / Year: 2025
Title: Structural asymmetry of HBsAg dictates the binding of HBV neutralization antibodies
Authors: He X
History
DepositionJul 31, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61003.png

Downloads & links

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Map

FileDownload / File: emd_61003.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 340 pix.
= 362.44 Å		1.07 Å/pix.
x 340 pix.
= 362.44 Å		1.07 Å/pix.
x 340 pix.
= 362.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.066 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-5.227402 - 6.406033
Average (Standard dev.)0.00077309617 (±0.04278735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 362.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61003_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: main map

Fileemd_61003_additional_1.map
Annotationmain map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61003_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61003_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HBV surface antigen dimer

EntireName: HBV surface antigen dimer
Components
  • Complex: HBV surface antigen dimer
    • Protein or peptide: Large envelope protein
  • Ligand: ZINC ION

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Supramolecule #1: HBV surface antigen dimer

SupramoleculeName: HBV surface antigen dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: HBV genotype D3 (virus)

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Macromolecule #1: Large envelope protein

MacromoleculeName: Large envelope protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: HBV genotype D3 (virus)
Molecular weightTheoretical: 25.430086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENITSGFLG PLLVLQAGFF LLTRILTIPQ SLDSWWTSLN FLGGTTVCLG QNSQSPTSNH SPTSCPPTCP GYRWMCLRRF IIFLFILLL CLIFLLVLLD YQGMLPVCPL IPGSSTTSTG PCRTCMTTAQ GTSMYPSCCC TKPSDGNCTC IPIPSSWAFG K FLWEWASA ...String:
MENITSGFLG PLLVLQAGFF LLTRILTIPQ SLDSWWTSLN FLGGTTVCLG QNSQSPTSNH SPTSCPPTCP GYRWMCLRRF IIFLFILLL CLIFLLVLLD YQGMLPVCPL IPGSSTTSTG PCRTCMTTAQ GTSMYPSCCC TKPSDGNCTC IPIPSSWAFG K FLWEWASA RFSWLSLLVP FVQWFVGLSP TVWLSVIWMM WYWGPSLYSI LSPFLPLLPI FFCLWVYI

UniProtKB: Large envelope protein

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 7.41
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1590360
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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