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- EMDB-37689: SARS-CoV-2 Omicron Spike in complex with XGV026 and XGV046 -

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Basic information

Entry
Database: EMDB / ID: EMD-37689
TitleSARS-CoV-2 Omicron Spike in complex with XGV026 and XGV046
Map data
Sample
  • Complex: SARS-CoV-2 Omicron Spike in complex with XGV043
KeywordsSARS-CoV-2 / Omicron / XGV026 / XGV046 / VIRUS
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsWang L
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: A third dose of inactivated vaccine augments the potency, breadth, and duration of anamnestic responses against SARS-CoV-2
Authors: Wang XX
History
DepositionOct 7, 2023-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37689.png

Downloads & links

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Map

FileDownload / File: emd_37689.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å		1.04 Å/pix.
x 300 pix.
= 312. Å

Surface

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Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009
Minimum - Maximum-0.023048291 - 0.051493805
Average (Standard dev.)0.00042862032 (±0.0023642664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 312.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37689_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_37689_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 : SARS-CoV-2 Omicron Spike in complex with XGV043

EntireName: SARS-CoV-2 Omicron Spike in complex with XGV043
Components
  • Complex: SARS-CoV-2 Omicron Spike in complex with XGV043

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Supramolecule #1: SARS-CoV-2 Omicron Spike in complex with XGV043

SupramoleculeName: SARS-CoV-2 Omicron Spike in complex with XGV043 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 27.0 µm / Nominal defocus min: 15.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

32478

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9617
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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