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- EMDB-35995: Cryo-EM structure of SARS-CoV-2 WT 6p spike protein in complex wi... -

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Entry
Database: EMDB / ID: EMD-35995
TitleCryo-EM structure of SARS-CoV-2 WT 6p spike protein in complex with W328-6H2 IgG
Map dataCryo-EM structure of SARS-CoV-2 WT 6p spike protein in complex with W328-6H2 IgG
Sample
  • Complex: Cryo-EM structure of SARS-CoV-2 WT 6p in complex with W328-6H2 IgG
    • Complex: Severe acute respiratory syndrome coronavirus 2 wild-type 6p
      • Complex: W328-6H2 IgG
KeywordsCryo-EM / Complex / SARS-CoV-2 WT / antibody / Homo sapiens / IgG / dimer / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 6.65 Å
AuthorsNan XY / Li YJ
Funding support1 items
OrganizationGrant numberCountry
Other government22277017
CitationJournal: Nat Commun / Year: 2024
Title: Exploring distinct modes of inter-spike cross-linking for enhanced neutralization by SARS-CoV-2 antibodies.
Authors: Xuanyu Nan / Yujie Li / Rui Zhang / Ruoke Wang / Niannian Lv / Jiayi Li / Yuanfang Chen / Bini Zhou / Yangjunqi Wang / Ziyi Wang / Jiayi Zhu / Jing Chen / Jinqian Li / Wenlong Chen / Qi ...Authors: Xuanyu Nan / Yujie Li / Rui Zhang / Ruoke Wang / Niannian Lv / Jiayi Li / Yuanfang Chen / Bini Zhou / Yangjunqi Wang / Ziyi Wang / Jiayi Zhu / Jing Chen / Jinqian Li / Wenlong Chen / Qi Zhang / Xuanling Shi / Changwen Zhao / Chunying Chen / Zhihua Liu / Yuliang Zhao / Dongsheng Liu / Xinquan Wang / Li-Tang Yan / Taisheng Li / Linqi Zhang / Yuhe R Yang /
Abstract: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its Omicron subvariants drastically amplifies transmissibility, infectivity, and immune escape, mainly due to their ...The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its Omicron subvariants drastically amplifies transmissibility, infectivity, and immune escape, mainly due to their resistance to most neutralizing antibodies. Thus, exploring the mechanisms underlying antibody evasion is crucial. Although the full-length native form of antibody, immunoglobulin G (IgG), offers valuable insights into the neutralization, structural investigations primarily focus on the fragment of antigen-binding (Fab). Here, we employ single-particle cryo-electron microscopy (cryo-EM) to characterize a W328-6H2 antibody, in its native IgG form complexed with severe acute respiratory syndrome (SARS), severe acute respiratory syndrome coronavirus 2 wild-type (WT) and Omicron variant BA.1 spike protein (S). Three high-resolution structures reveal that the full-length IgG forms a centered head-to-head dimer of trimer when binds fully stoichiometrically with both SARS and WT S, while adopting a distinct offset configuration with Omicron BA.1 S. Combined with functional assays, our results suggest that, beyond the binding affinity between the RBD epitope and Fab, the higher-order architectures of S trimer and full-length IgG play an additional role in neutralization, enriching our understanding of enhanced neutralization by SARS-CoV-2 antibodies.
History
DepositionApr 24, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35995.png

Downloads & links

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Map

FileDownload / File: emd_35995.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of SARS-CoV-2 WT 6p spike protein in complex with W328-6H2 IgG
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 600 pix.
= 582. Å		0.97 Å/pix.
x 600 pix.
= 582. Å		0.97 Å/pix.
x 600 pix.
= 582. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.41417584 - 0.9455234
Average (Standard dev.)-0.00025976627 (±0.028962085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 582.0 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 WT 6p spike protein...

Fileemd_35995_half_map_1.map
AnnotationCryo-EM structure of SARS-CoV-2 WT 6p spike protein in complex with W328-6H2 IgG
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 WT 6p spike protein...

Fileemd_35995_half_map_2.map
AnnotationCryo-EM structure of SARS-CoV-2 WT 6p spike protein in complex with W328-6H2 IgG
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 WT 6p in complex with W328-6H2 IgG

EntireName: Cryo-EM structure of SARS-CoV-2 WT 6p in complex with W328-6H2 IgG
Components
  • Complex: Cryo-EM structure of SARS-CoV-2 WT 6p in complex with W328-6H2 IgG
    • Complex: Severe acute respiratory syndrome coronavirus 2 wild-type 6p
      • Complex: W328-6H2 IgG

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Supramolecule #1: Cryo-EM structure of SARS-CoV-2 WT 6p in complex with W328-6H2 IgG

SupramoleculeName: Cryo-EM structure of SARS-CoV-2 WT 6p in complex with W328-6H2 IgG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Cryo-EM structure of SARS-CoV-2 WT 6p spike protein in complex with W328-6H2 IgG
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Severe acute respiratory syndrome coronavirus 2 wild-type 6p

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 wild-type 6p
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 / Details: SARS-CoV-2 WT 6p
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: W328-6H2 IgG

SupramoleculeName: W328-6H2 IgG / type: complex / ID: 3 / Parent: 2 / Macromolecule list: #3 / Details: W328-6H2 IgG
Source (natural)Organism: 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

Concentration0.3 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 2537 / Average electron dose: 50.0 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: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 141485
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23820
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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