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- EMDB-19438: Hepatitis B virus core antigen (HBc) with insertion of SpyCatcher... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-19438
TitleHepatitis B virus core antigen (HBc) with insertion of SpyCatcher at MIR and conjugated to single chain Fc domain
Map data
Sample
  • Virus: Hepatitis B virus
KeywordsHBc / Fc domain / icosahedron / T=3 / VIRUS LIKE PARTICLE
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsPetrova E / Teixeira AI / Hallberg BM
Funding support Sweden, 1 items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2017.0114 Sweden
CitationJournal: To Be Published
Title: Hepatitis B virus core antigen (HBc) with insertion of SpyCatcher at MIR and conjugated to single chain Fc domain
Authors: Petrova E / Teixeira AI / Hallberg BM
History
DepositionJan 17, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19438.png

Downloads & links

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Map

FileDownload / File: emd_19438.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 500 pix.
= 850. Å		1.7 Å/pix.
x 500 pix.
= 850. Å		1.7 Å/pix.
x 500 pix.
= 850. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-4.197523 - 8.246153
Average (Standard dev.)-0.00020261105 (±0.19235288)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 850.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_19438_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_19438_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 : Hepatitis B virus

EntireName: Hepatitis B virus
Components
  • Virus: Hepatitis B virus

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Supramolecule #1: Hepatitis B virus

SupramoleculeName: Hepatitis B virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.5 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: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 96073
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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