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- EMDB-43326: Negative Stain EM Reconstructions of SARS-CoV-2 spike proteins mi... -

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Basic information

Entry
Database: EMDB / ID: EMD-43326
TitleNegative Stain EM Reconstructions of SARS-CoV-2 spike proteins mixed with polyclonal antibodies from donor 4.
Map dataNegative Stain EM reconstruction of XBB.1.5 spike protein when mixed with polyclonal fabs from donor 4 (apo - C1 symmetry)
Sample
  • Complex: SARS-CoV-2 XBB.1.5 spike protein trimer
KeywordsComplex / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsMannar D / Zhu X / Saville J / Poloni C / Bezeruk A / Tidey K / Ahmed S / Vahdatihassani F / Cholak S / Cook L ...Mannar D / Zhu X / Saville J / Poloni C / Bezeruk A / Tidey K / Ahmed S / Vahdatihassani F / Cholak S / Cook L / Steiner TS / Subramaniam S
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canada Excellence Research Chair Award Canada
CitationJournal: To Be Published
Title: SARS-CoV-2 XBB.1.5 Spike Protein: Altered Receptor Binding, Antibody Evasion, and Retention of T Cell Recognition
Authors: Mannar D / Saville J / Poloni C / Zhu X / Bezeruk A / Tidey K / Ahmed S / Tuttle K / Vahdatihassani F / Cholak S / Cook L / Steiner TS / Subramaniam S
History
DepositionJan 9, 2024-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43326.png

Downloads & links

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Map

FileDownload / File: emd_43326.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative Stain EM reconstruction of XBB.1.5 spike protein when mixed with polyclonal fabs from donor 4 (apo - C1 symmetry)
Voxel sizeX=Y=Z: 1.9 Å
Density
Contour LevelBy AUTHOR: 0.244
Minimum - Maximum-1.2562463 - 2.4392776
Average (Standard dev.)-0.001294204 (±0.060087632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 570.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Negative Stain EM reconstruction of WT spike protein...

Fileemd_43326_additional_1.map
AnnotationNegative Stain EM reconstruction of WT spike protein when mixed with polyclonal fabs from donor 4 (RBD up directed - C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Negative Stain EM reconstruction of XBB.1.5 spike protein...

Fileemd_43326_additional_2.map
AnnotationNegative Stain EM reconstruction of XBB.1.5 spike protein when mixed with polyclonal IgG from donor 4 (RBD up directed - C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Negative Stain EM reconstruction of WT spike protein...

Fileemd_43326_additional_3.map
AnnotationNegative Stain EM reconstruction of WT spike protein when mixed with polyclonal fabs from donor 4 (RBD up directed - C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Negative Stain EM reconstruction of WT spike protein...

Fileemd_43326_additional_4.map
AnnotationNegative Stain EM reconstruction of WT spike protein when mixed with polyclonal fabs from donor 4 (RBD up directed x 2 - C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Negative Stain EM reconstruction of WT spike protein...

Fileemd_43326_additional_5.map
AnnotationNegative Stain EM reconstruction of WT spike protein when mixed with polyclonal fabs from donor 4 (NTD bottom face directed - C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43326_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43326_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 XBB.1.5 spike protein trimer

EntireName: SARS-CoV-2 XBB.1.5 spike protein trimer
Components
  • Complex: SARS-CoV-2 XBB.1.5 spike protein trimer

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Supramolecule #1: SARS-CoV-2 XBB.1.5 spike protein trimer

SupramoleculeName: SARS-CoV-2 XBB.1.5 spike protein trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 82636

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