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- EMDB-34339: Prefusion spike protein of BA.1.1 with one-RBD-up conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-34339
TitlePrefusion spike protein of BA.1.1 with one-RBD-up conformation
Map dataPrefusion spike of BA.1.1 with one-RBD-up conformation
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: 9.1 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_34339.png

Downloads & links

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Map

FileDownload / File: emd_34339.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrefusion spike of BA.1.1 with one-RBD-up conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.66 Å/pix.
x 96 pix.
= 255.36 Å		2.66 Å/pix.
x 96 pix.
= 255.36 Å		2.66 Å/pix.
x 96 pix.
= 255.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.8376582 - 1.4767799
Average (Standard dev.)0.0101666665 (±0.081010185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 255.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_34339_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_34339_half_map_2.map
Annotationhalf 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 3575
ExtractionNumber tomograms: 124 / Number images used: 28584
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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