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- EMDB-66006: Subtomogram averaging of SARS-CoV-2 spike-S309-IgG solo structure... -

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Basic information

Entry
Database: EMDB / ID: EMD-66006
TitleSubtomogram averaging of SARS-CoV-2 spike-S309-IgG solo structure in 1-RBD-up conformation
Map data
Sample
  • Virus: Severe acute respiratory syndrome coronavirus 2
KeywordsIgG / spike / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsubtomogram averaging / cryo EM / Resolution: 14.5 Å
AuthorsSong Y / Huang Q / Li S
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-ET of IgG bivalent binding on SARS-CoV-2 provides structural basis for antibody avidity.
Authors: Hangping Yao / Yutong Song / Qi Huang / Miaojin Zhu / Jiaming Liang / Zheyuan Zhang / Xiaodi Zhang / Dongyang Dong / Danrong Shi / Zhigang Wu / Xiangyun Lu / Haibo Wu / Yong Chen / Sai Li /
Abstract: The bivalent nature of IgG antibodies can enhance its neutralization potency against enveloped viruses; however, on-virion structural details of IgG bivalent binding with antigens remain elusive. ...The bivalent nature of IgG antibodies can enhance its neutralization potency against enveloped viruses; however, on-virion structural details of IgG bivalent binding with antigens remain elusive. Here we investigate how two potent IgGs P17 and S309 interact with S-trimers on the SARS-CoV-2 surface by cryo-ET. We find both IgGs exploit the mobility of S-trimers to form diverse configurations of S-IgG dimer-of-trimers, which oligomerize into higher-order patterns. Specifically, P17 stabilizes S-trimers into linear assemblies within minutes, whereas S309 primarily stabilizes S-trimer into circular assemblies that extend into lattice-like structures. Both assembly patterns effectively activate complement cascade. Additionally, both IgGs can facilitate inter-virion coupling through bivalent binding of opposing S-trimers, potentially enhancing immune recognition and clearance. These findings establish a structural framework for understanding IgG avidity in neutralizing enveloped viruses and offer valuable insights for antibody engineering and vaccine design.
History
DepositionAug 29, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66006.png

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Map

FileDownload / File: emd_66006.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
2.72 Å/pix.
x 176 pix.
= 478.72 Å		2.72 Å/pix.
x 176 pix.
= 478.72 Å		2.72 Å/pix.
x 176 pix.
= 478.72 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.72 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 1.2
Minimum - Maximum-6.792127 - 7.541381
Average (Standard dev.)0.0012702381 (±0.41935572)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions176176176
Spacing176176176
CellA=B=C: 478.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66006_msk_1.map
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Half map: #1

Fileemd_66006_half_map_1.map
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Half map: #2

Fileemd_66006_half_map_2.map
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Sample components

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Entire : Severe acute respiratory syndrome coronavirus 2

EntireName: Severe acute respiratory syndrome coronavirus 2
Components
  • Virus: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #1: Severe acute respiratory syndrome coronavirus 2

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2697049
Sci species name: Severe acute respiratory syndrome coronavirus 2
Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 64000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 14.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 4237
ExtractionNumber tomograms: 33 / Number images used: 11747 / Software - Name: Dynamo
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: OTHER / Software - Name: Dynamo
FSC plot (resolution estimation)

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