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- EMDB-33415: Cryo-EM structure of SARS-CoV-2 spike protein in complex with nan... -

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Entry
Database: EMDB / ID: EMD-33415
TitleCryo-EM structure of SARS-CoV-2 spike protein in complex with nanobody C5G2
Map dataCryo-EM density map of SARS-CoV-2 spike protein in complex with C5G2
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 spike protein in complex with nanobody C5G2
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.51 Å
AuthorsLiu L / Sun H / Jiang Y / Liu X / Zhao D / Zheng Q / Li S / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: J Nanobiotechnology / Year: 2022
Title: A potent synthetic nanobody with broad-spectrum activity neutralizes SARS-CoV-2 virus and the Omicron variant BA.1 through a unique binding mode.
Authors: Dongping Zhao / Liqin Liu / Xinlin Liu / Jinlei Zhang / Yuqing Yin / Linli Luan / Dingwen Jiang / Xiong Yang / Lei Li / Hualong Xiong / Dongming Xing / Qingbing Zheng / Ningshao Xia / Yuyong ...Authors: Dongping Zhao / Liqin Liu / Xinlin Liu / Jinlei Zhang / Yuqing Yin / Linli Luan / Dingwen Jiang / Xiong Yang / Lei Li / Hualong Xiong / Dongming Xing / Qingbing Zheng / Ningshao Xia / Yuyong Tao / Shaowei Li / Haiming Huang /
Abstract: The major challenge to controlling the COVID pandemic is the rapid mutation rate of the SARS-CoV-2 virus, leading to the escape of the protection of vaccines and most of the neutralizing antibodies ...The major challenge to controlling the COVID pandemic is the rapid mutation rate of the SARS-CoV-2 virus, leading to the escape of the protection of vaccines and most of the neutralizing antibodies to date. Thus, it is essential to develop neutralizing antibodies with broad-spectrum activity targeting multiple SARS-CoV-2 variants. Here, we report a synthetic nanobody (named C5G2) obtained by phage display and subsequent antibody engineering. C5G2 has a single-digit nanomolar binding affinity to the RBD domain and inhibits its binding to ACE2 with an IC of 3.7 nM. Pseudovirus assays indicated that monovalent C5G2 could protect the cells from infection with SARS-CoV-2 wild-type virus and most of the viruses of concern, i.e., Alpha, Beta, Gamma and Omicron variants. Strikingly, C5G2 has the highest potency against Omicron BA.1 among all the variants, with an IC of 4.9 ng/mL. The cryo-EM structure of C5G2 in complex with the spike trimer showed that C5G2 binds to RBD mainly through its CDR3 at a conserved region that does not overlap with the ACE2 binding surface. Additionally, C5G2 binds simultaneously to the neighboring NTD domain of the spike trimer through the same CDR3 loop, which may further increase its potency against viral infection. Third, the steric hindrance caused by FR2 of C5G2 could inhibit the binding of ACE2 to RBD as well. Thus, this triple-function nanobody may serve as an effective drug for prophylaxis and therapy against Omicron as well as future variants.
History
DepositionMay 10, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateApr 19, 2023-
Current statusApr 19, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33415.png

Downloads & links

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Map

FileDownload / File: emd_33415.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map of SARS-CoV-2 spike protein in complex with C5G2
Voxel sizeX=Y=Z: 0.778 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.44254017 - 0.7420353
Average (Standard dev.)-0.00031585456 (±0.013978335)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 398.336 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM density map of SARS-CoV-2 spike protein in complex with C5G2

Fileemd_33415_half_map_1.map
AnnotationCryo-EM density map of SARS-CoV-2 spike protein in complex with C5G2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM density map of SARS-CoV-2 spike protein in complex with C5G2

Fileemd_33415_half_map_2.map
AnnotationCryo-EM density map of SARS-CoV-2 spike protein in complex with C5G2
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 spike protein in complex with nan...

EntireName: Cryo-EM structure of SARS-CoV-2 spike protein in complex with nanobody C5G2
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 spike protein in complex with nanobody C5G2

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Supramolecule #1: Cryo-EM structure of SARS-CoV-2 spike protein in complex with nan...

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 spike protein in complex with nanobody C5G2
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3
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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k 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: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120400
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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