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- EMDB-34341: Postfusion spike of BA.2.3 -

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Basic information

Entry
Database: EMDB / ID: EMD-34341
TitlePostfusion spike of BA.2.3
Map dataPostfusion spike of BA.2.3
Sample
  • Complex: Severe acute respiratory syndrome coronavirus 2
KeywordsCryo-ET / Subtomogram averaging / Omicron / prefusion spike / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 28.0 Å
AuthorsGao YZ / Ma XY / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)818702246, 82070329 China
CitationJournal: Signal Transduct Target Ther / Year: 2023
Title: Structural characteristics of the SARS-CoV-2 Omicron lineages BA.1 and BA.2 virions.
Authors: Xiaoyu Ma / Yanqun Wang / Yuanzhu Gao / Yiliang Wang / An Yan / Jiantao Chen / Lu Zhang / Peiyi Wang / Jincun Zhao / Zheng Liu /
History
DepositionSep 19, 2022-
Header (metadata) releaseSep 20, 2023-
Map releaseSep 20, 2023-
UpdateAug 21, 2024-
Current statusAug 21, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34341.png

Downloads & links

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Map

FileDownload / File: emd_34341.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostfusion spike of BA.2.3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.33 Å/pix.
x 64 pix.
= 341.248 Å		5.33 Å/pix.
x 64 pix.
= 341.248 Å		5.33 Å/pix.
x 64 pix.
= 341.248 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.25881776 - 0.5064619
Average (Standard dev.)-0.029516818 (±0.057030328)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 341.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Postfusion spike of BA.2.3, half map

Fileemd_34341_half_map_1.map
AnnotationPostfusion spike of BA.2.3, half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Postfusion spike of BA.2.3, half map

Fileemd_34341_half_map_2.map
AnnotationPostfusion spike of BA.2.3, half 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 : Severe acute respiratory syndrome coronavirus 2

EntireName: Severe acute respiratory syndrome coronavirus 2
Components
  • Complex: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #1: Severe acute respiratory syndrome coronavirus 2

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: BA.1.1

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
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: 2.92 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 139
ExtractionNumber tomograms: 92 / Number images used: 139
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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