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- EMDB-35962: Immune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p... -

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Basic information

Entry
Database: EMDB / ID: EMD-35962
TitleImmune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein added BS3 crosslinker
Map dataImmune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein added BS3 cross-linker
Sample
  • Complex: Omicron BA.1 6p in complex with W328-6H2 Fab
    • Complex: Severe acute respiratory syndrome coronavirus 2 Omicron BA.1 6p
      • Complex: W328-6H2 Fab
KeywordsComplex / Omicron BA.1 6p / antibody / Homo sapiens / RBD / Fab / Cross-linker / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsNan XY / Li YJ / Li JY
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 17, 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_35962.png

Downloads & links

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Map

FileDownload / File: emd_35962.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationImmune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein added BS3 cross-linker
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.21 Å/pix.
x 192 pix.
= 424.32 Å		2.21 Å/pix.
x 192 pix.
= 424.32 Å		2.21 Å/pix.
x 192 pix.
= 424.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0227
Minimum - Maximum-0.025498219 - 0.08399581
Average (Standard dev.)0.00018370413 (±0.0049117645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 424.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Immune complex of W328-6H2 Fab binding the RBD...

Fileemd_35962_half_map_1.map
AnnotationImmune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein added BS3 cross-linker
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Immune complex of W328-6H2 Fab binding the RBD...

Fileemd_35962_half_map_2.map
AnnotationImmune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein added BS3 cross-linker
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Omicron BA.1 6p in complex with W328-6H2 Fab

EntireName: Omicron BA.1 6p in complex with W328-6H2 Fab
Components
  • Complex: Omicron BA.1 6p in complex with W328-6H2 Fab
    • Complex: Severe acute respiratory syndrome coronavirus 2 Omicron BA.1 6p
      • Complex: W328-6H2 Fab

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Supramolecule #1: Omicron BA.1 6p in complex with W328-6H2 Fab

SupramoleculeName: Omicron BA.1 6p in complex with W328-6H2 Fab / type: complex / ID: 1 / Parent: 0
Details: Immune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein added BS3 cross-linker
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Severe acute respiratory syndrome coronavirus 2 Omicron BA.1 6p

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 Omicron BA.1 6p
type: complex / ID: 2 / Parent: 1 / Details: Omicron BA.1 6p
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: W328-6H2 Fab

SupramoleculeName: W328-6H2 Fab / type: complex / ID: 3 / Parent: 2 / Details: W328-6H2 Fab
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.015 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeJEOL 2100F
Image recordingFilm or detector model: OTHER / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm

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Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 7266
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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