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- EMDB-32518: Omicron spike in complex with human neutralizing antibody XMA01 -

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Entry
Database: EMDB / ID: EMD-32518
TitleOmicron spike in complex with human neutralizing antibody XMA01
Map dataOmicron spike in complex with human neutralizing antibody 6F9
Sample
  • Complex: Omicron spike in complex with human neutralizing antibody XMA01
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.23 Å
AuthorsZheng Q / Li S / Sun H / Zheng Z / Wang S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2022
Title: Three SARS-CoV-2 antibodies provide broad and synergistic neutralization against variants of concern, including Omicron.
Authors: Siling Wang / Hui Sun / Yali Zhang / Lunzhi Yuan / Yizhen Wang / Tianying Zhang / Shaojuan Wang / Jinlei Zhang / Hai Yu / Hualong Xiong / Zimin Tang / Liqin Liu / Yang Huang / Xiuting Chen / ...Authors: Siling Wang / Hui Sun / Yali Zhang / Lunzhi Yuan / Yizhen Wang / Tianying Zhang / Shaojuan Wang / Jinlei Zhang / Hai Yu / Hualong Xiong / Zimin Tang / Liqin Liu / Yang Huang / Xiuting Chen / Tingting Li / Dong Ying / Chang Liu / Zihao Chen / Quan Yuan / Jun Zhang / Tong Cheng / Shaowei Li / Yi Guan / Qingbing Zheng / Zizheng Zheng / Ningshao Xia /
Abstract: The rapidly spreading Omicron variant is highly resistant to vaccines, convalescent sera, and neutralizing antibodies (nAbs), highlighting the urgent need for potent therapeutic nAbs. Here, a panel ...The rapidly spreading Omicron variant is highly resistant to vaccines, convalescent sera, and neutralizing antibodies (nAbs), highlighting the urgent need for potent therapeutic nAbs. Here, a panel of human nAbs from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) convalescent patients show diverse neutralization against Omicron, of which XMA01 and XMA04 maintain nanomolar affinities and excellent neutralization (half maximal inhibitory concentration [IC50]: ∼20 ng/mL). nAb XMA09 shows weak but unattenuated neutralization against all variants of concern (VOCs) as well as SARS-CoV. Structural analysis reveals that the above three antibodies could synergistically bind to the receptor-binding domains (RBDs) of both wild-type and Omicron spikes and defines the critical determinants for nAb-mediated broad neutralizations. Three nAbs confer synergistic neutralization against Omicron, resulting from the inter-antibody interaction between XMA04 and XMA01(or XMA09). Furthermore, the XMA01/XMA04 cocktail provides synergistic protection against Beta and Omicron variant infections in hamsters. In summary, our results provide insights for the rational design of antibody cocktail therapeutics or universal vaccines against Omicron.
History
DepositionJan 1, 2022-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJun 22, 2022-
Current statusJun 22, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32518.png

Downloads & links

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Map

FileDownload / File: emd_32518.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOmicron spike in complex with human neutralizing antibody 6F9
Voxel sizeX=Y=Z: 1.556 Å
Density
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.11652003 - 0.43852913
Average (Standard dev.)-0.0003093694 (±0.016939064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 448.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Omicron spike in complex with human neutralizing antibody XMA01

EntireName: Omicron spike in complex with human neutralizing antibody XMA01
Components
  • Complex: Omicron spike in complex with human neutralizing antibody XMA01

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Supramolecule #1: Omicron spike in complex with human neutralizing antibody XMA01

SupramoleculeName: Omicron spike in complex with human neutralizing antibody XMA01
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Homo sapiens (human)

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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: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37785
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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