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- EMDB-33225: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-33225
TitleCryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Map dataCryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsGeorge FG / Sheng L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell / Year: 2022
Title: Protective prototype-Beta and Delta-Omicron chimeric RBD-dimer vaccines against SARS-CoV-2.
Authors: Kun Xu / Ping Gao / Sheng Liu / Shuaiyao Lu / Wenwen Lei / Tianyi Zheng / Xueyuan Liu / Yufeng Xie / Zhennan Zhao / Shuxin Guo / Cong Tang / Yun Yang / Wenhai Yu / Junbin Wang / Yanan Zhou / ...Authors: Kun Xu / Ping Gao / Sheng Liu / Shuaiyao Lu / Wenwen Lei / Tianyi Zheng / Xueyuan Liu / Yufeng Xie / Zhennan Zhao / Shuxin Guo / Cong Tang / Yun Yang / Wenhai Yu / Junbin Wang / Yanan Zhou / Qing Huang / Chuanyu Liu / Yaling An / Rong Zhang / Yuxuan Han / Minrun Duan / Shaofeng Wang / Chenxi Yang / Changwei Wu / Xiaoya Liu / Guangbiao She / Yan Liu / Xin Zhao / Ke Xu / Jianxun Qi / Guizhen Wu / Xiaozhong Peng / Lianpan Dai / Peiyi Wang / George F Gao /
Abstract: Breakthrough infections by SARS-CoV-2 variants become the global challenge for pandemic control. Previously, we developed the protein subunit vaccine ZF2001 based on the dimeric receptor-binding ...Breakthrough infections by SARS-CoV-2 variants become the global challenge for pandemic control. Previously, we developed the protein subunit vaccine ZF2001 based on the dimeric receptor-binding domain (RBD) of prototype SARS-CoV-2. Here, we developed a chimeric RBD-dimer vaccine approach to adapt SARS-CoV-2 variants. A prototype-Beta chimeric RBD-dimer was first designed to adapt the resistant Beta variant. Compared with its homotypic forms, the chimeric vaccine elicited broader sera neutralization of variants and conferred better protection in mice. The protection of the chimeric vaccine was further verified in macaques. This approach was generalized to develop Delta-Omicron chimeric RBD-dimer to adapt the currently prevalent variants. Again, the chimeric vaccine elicited broader sera neutralization of SARS-CoV-2 variants and conferred better protection against challenge by either Delta or Omicron SARS-CoV-2 in mice. The chimeric approach is applicable for rapid updating of immunogens, and our data supported the use of variant-adapted multivalent vaccine against circulating and emerging variants.
History
DepositionApr 17, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateMay 3, 2023-
Current statusMay 3, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33225.png

Downloads & links

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Map

FileDownload / File: emd_33225.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 320 pix.
= 211.2 Å		0.66 Å/pix.
x 320 pix.
= 211.2 Å		0.66 Å/pix.
x 320 pix.
= 211.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.111364536 - 0.23417038
Average (Standard dev.)-0.00011597294 (±0.018531024)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 211.20001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab

Fileemd_33225_half_map_1.map
AnnotationCryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab

Fileemd_33225_half_map_2.map
AnnotationCryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab

EntireName: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab

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Supramolecule #1: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 prototype RBD-dimer bound to CB6 Fab
type: complex / ID: 1 / Chimera: Yes / 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 K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.39 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26842
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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