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- EMDB-61013: 3x2mer of HBsAg in recombinant spherical SVP -

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Basic information

Entry
Database: EMDB / ID: EMD-61013
Title3x2mer of HBsAg in recombinant spherical SVP
Map dataMain map of 3x2mer of HBsAg in spherical SVP
Sample
  • Complex: HBV surface antigen dimer
KeywordsHBV / HBsAg / VIRAL PROTEIN / SVP
Biological speciesHBV genotype D3 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsChen L / He X / Kang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31821091 China
CitationJournal: Cell Discov / Year: 2025
Title: Structure of small HBV surface antigen reveals mechanism of dimer formation.
Authors: Xiao He / Yunlu Kang / Weiyu Tao / Jiaxuan Xu / Xiaoyu Liu / Lei Chen /
History
DepositionJul 31, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61013.png

Downloads & links

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Map

FileDownload / File: emd_61013.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map of 3x2mer of HBsAg in spherical SVP
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-2.6076934 - 3.598083
Average (Standard dev.)0.00088334444 (±0.045009736)
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_61013_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of 3x2mer of HBsAg in spherical SVP

Fileemd_61013_half_map_1.map
AnnotationHalf map A of 3x2mer of HBsAg in spherical SVP
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of 3x2mer of HBsAg in spherical SVP

Fileemd_61013_half_map_2.map
AnnotationHalf map B of 3x2mer of HBsAg in spherical SVP
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

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Supramolecule #1: HBV surface antigen dimer

SupramoleculeName: HBV surface antigen dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: HBV genotype D3 (virus)

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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 530120
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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