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

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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: Nat Commun / Year: 2024
Title: Altered receptor binding, antibody evasion and retention of T cell recognition by the SARS-CoV-2 XBB.1.5 spike protein.
Authors: Dhiraj Mannar / James W Saville / Chad Poloni / Xing Zhu / Alison Bezeruk / Keith Tidey / Sana Ahmed / Katharine S Tuttle / Faezeh Vahdatihassani / Spencer Cholak / Laura Cook / Theodore S ...Authors: Dhiraj Mannar / James W Saville / Chad Poloni / Xing Zhu / Alison Bezeruk / Keith Tidey / Sana Ahmed / Katharine S Tuttle / Faezeh Vahdatihassani / Spencer Cholak / Laura Cook / Theodore S Steiner / Sriram Subramaniam /
Abstract: The XBB.1.5 variant of SARS-CoV-2 has rapidly achieved global dominance and exhibits a high growth advantage over previous variants. Preliminary reports suggest that the success of XBB.1.5 stems from ...The XBB.1.5 variant of SARS-CoV-2 has rapidly achieved global dominance and exhibits a high growth advantage over previous variants. Preliminary reports suggest that the success of XBB.1.5 stems from mutations within its spike glycoprotein, causing immune evasion and enhanced receptor binding. We present receptor binding studies that demonstrate retention of binding contacts with the human ACE2 receptor and a striking decrease in binding to mouse ACE2 due to the revertant R493Q mutation. Despite extensive evasion of antibody binding, we highlight a region on the XBB.1.5 spike protein receptor binding domain (RBD) that is recognized by serum antibodies from a donor with hybrid immunity, collected prior to the emergence of the XBB.1.5 variant. T cell assays reveal high frequencies of XBB.1.5 spike-specific CD4 and CD8 T cells amongst donors with hybrid immunity, with the CD4 T cells skewed towards a Th1 cell phenotype and having attenuated effector cytokine secretion as compared to ancestral spike protein-specific cells. Thus, while the XBB.1.5 variant has retained efficient human receptor binding and gained antigenic alterations, it remains susceptible to recognition by T cells induced via vaccination and previous infection.
History
DepositionJan 9, 2024-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing 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)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.9 Å/pix.
x 300 pix.
= 570. Å		1.9 Å/pix.
x 300 pix.
= 570. Å		1.9 Å/pix.
x 300 pix.
= 570. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.9 Å
Density

Histogram

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

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Image processing

Startup modelType of model: NONE
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
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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