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- EMDB-60863: Cryo-EM structure of SARS-CoV-2 WT spike protein in complex with ... -

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Entry
Database: EMDB / ID: EMD-60863
TitleCryo-EM structure of SARS-CoV-2 WT spike protein in complex with three-nAb 8H12, 3E2 and 1C4
Map data
Sample
  • Complex: SARS-CoV-2 WT spike protein in complex with three-nAb 8H12, 3E2 and 1C4
    • Complex: Spike protein
    • Complex: The Fab fragments of three-nAb 8H12, 3E2 and 1C4
KeywordsCryo-EM / SARs-CoV-2 / antibody / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMus musculus (house mouse) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.76 Å
AuthorsSun H / Jiang Y / Li S / Zheng Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: PLoS Pathog / Year: 2025
Title: Engineering a multivalent antibody nanoparticle to overcome SARS-CoV-2 Omicron immune evasion.
Authors: Hui Sun / Yanan Jiang / Miaolin Lan / Ming Zhou / Gangshun Yi / Juan Shen / Tingting Deng / Liqin Liu / Yang Huang / Yu Li / Jinfu Su / Yanling Lin / Zhenqin Chen / Lizhi Zhou / Tingting Li ...Authors: Hui Sun / Yanan Jiang / Miaolin Lan / Ming Zhou / Gangshun Yi / Juan Shen / Tingting Deng / Liqin Liu / Yang Huang / Yu Li / Jinfu Su / Yanling Lin / Zhenqin Chen / Lizhi Zhou / Tingting Li / Hai Yu / Tong Cheng / Yali Zhang / Lunzhi Yuan / Shaowei Li / Ying Gu / Peijun Zhang / Ningshao Xia / Qingbing Zheng /
Abstract: The rapid evolution of SARS-CoV-2 and the subsequent emergence of Omicron subvariants pose significant challenges to the efficacy of existing vaccines and therapeutics, including those previously ...The rapid evolution of SARS-CoV-2 and the subsequent emergence of Omicron subvariants pose significant challenges to the efficacy of existing vaccines and therapeutics, including those previously reported most broad neutralizing antibodies (bnAbs). Here, we investigated the molecular basis of the altered neutralization profile of a bnAb, 1C4, against recent variants. 1C4 is effective against early variants from Alpha to Omicron BQ.1, but is circumvented by BQ.1.1, XBB and thereafter variants, primarily due to an additional R346T mutation that diminishes its binding affinity. Cryo-electron microscopy analysis revealed that despite the loss of neutralizing potency, 1C4 retained residual binding to the spike protein of immune-evasive variants such as XBB, which harbor altered receptor-binding domain (RBD). Furthermore, 1C4 exhibited a diminished capacity to inhibit ACE2 engagement with Omicron variants, amplifying the intricacies of viral immune evasion tactics. To address this, we employed the mi3-SpyCatcher-based nanoparticle to polymerize 1C4 (mi3-1C4), which reestablished the neutralization potency against recent variants by enhancing avidity via multivalent binding. Such multivalent binding can promote efficient spike aggregation as well as viral cross-linking, thereby providing enhanced protection against both the infection of Beta and XBB variants in a hamster model. Together, our findings delineate the molecular landscape of immune evasion by neutralizing antibodies and provide strategic insight for the adaptation of antibody engineering to keep pace with viral evolution.
History
DepositionJul 20, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60863.png

Downloads & links

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Map

FileDownload / File: emd_60863.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 576 pix.
= 448.128 Å		0.78 Å/pix.
x 576 pix.
= 448.128 Å		0.78 Å/pix.
x 576 pix.
= 448.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.11123299 - 0.30220598
Average (Standard dev.)-0.00012744592 (±0.008870742)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 448.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60863_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60863_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : SARS-CoV-2 WT spike protein in complex with three-nAb 8H12, 3E2 a...

EntireName: SARS-CoV-2 WT spike protein in complex with three-nAb 8H12, 3E2 and 1C4
Components
  • Complex: SARS-CoV-2 WT spike protein in complex with three-nAb 8H12, 3E2 and 1C4
    • Complex: Spike protein
    • Complex: The Fab fragments of three-nAb 8H12, 3E2 and 1C4

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Supramolecule #1: SARS-CoV-2 WT spike protein in complex with three-nAb 8H12, 3E2 a...

SupramoleculeName: SARS-CoV-2 WT spike protein in complex with three-nAb 8H12, 3E2 and 1C4
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: Spike protein

SupramoleculeName: Spike protein / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: The Fab fragments of three-nAb 8H12, 3E2 and 1C4

SupramoleculeName: The Fab fragments of three-nAb 8H12, 3E2 and 1C4 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

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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: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90363
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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