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- EMDB-36122: Cryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (l... -

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Entry
Database: EMDB / ID: EMD-36122
TitleCryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)
Map dataCryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)
Sample
  • Complex: Cryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)
    • Complex: Severe acute respiratory syndrome coronavirus 2 Omicron BA.1 6p
    • Complex: W328-6H2 IgG
KeywordsCryo-EM / Complex / Omicron BA.1 / antibody / Homo sapiens / IgG / RBD / local refinement / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus ...Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 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
DepositionMay 5, 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_36122.png

Downloads & links

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Map

FileDownload / File: emd_36122.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 320 pix.
= 310.4 Å		0.97 Å/pix.
x 320 pix.
= 310.4 Å		0.97 Å/pix.
x 320 pix.
= 310.4 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: 0.586
Minimum - Maximum-1.7039305 - 2.6230242
Average (Standard dev.)0.0011597684 (±0.04271991)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 310.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Cryo-EM structure of Omicron BA.1 RBD in complex...

Fileemd_36122_half_map_1.map
AnnotationCryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of Omicron BA.1 RBD in complex...

Fileemd_36122_half_map_2.map
AnnotationCryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)
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 Omicron BA.1 RBD in complex with W328-6H2 (l...

EntireName: Cryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)
Components
  • Complex: Cryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)
    • Complex: Severe acute respiratory syndrome coronavirus 2 Omicron BA.1 6p
    • Complex: W328-6H2 IgG

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Supramolecule #1: Cryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (l...

SupramoleculeName: Cryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Cryo-EM structure of Omicron BA.1 RBD in complex with W328-6H2 (local refinement)
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 / Macromolecule list: #2 / Details: Omicron BA.1 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: 1 / 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 / 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: 2567 / 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: 148965
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44293
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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