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- EMDB-73273: SARS-CoV-2 Omicron BA.1 spike, 1-RBD-up -

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Basic information

Entry
Database: EMDB / ID: EMD-73273
TitleSARS-CoV-2 Omicron BA.1 spike, 1-RBD-up
Map data
Sample
  • Complex: SARS-CoV-2 Omicron BA.1 spike
KeywordsSARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsWang Y / Hu Y / Leiman P / Xie X
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM139034 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM158090 United States
CitationJournal: PLoS Pathog / Year: 2026
Title: Neutralization of SARS-CoV-2 by IgM-14 via engagement of two distinct spike epitopes.
Authors: Yan Wang / Yanping Hu / Zhiqiang Ku / Jason Yeung / Jing Zou / Michael Woodson / Nikolai S Prokhorov / Ekaterina S Knyazhanskaya / Haiqing Zhao / Michael B Sherman / Zhiqiang An / Stephen F ...Authors: Yan Wang / Yanping Hu / Zhiqiang Ku / Jason Yeung / Jing Zou / Michael Woodson / Nikolai S Prokhorov / Ekaterina S Knyazhanskaya / Haiqing Zhao / Michael B Sherman / Zhiqiang An / Stephen F Carroll / Pei-Yong Shi / Petr G Leiman / Xuping Xie /
Abstract: Engineered immunoglobulin M (IgM) antibodies typically exhibit superior neutralization potency and avidity compared to their parental IgG counterparts, primarily due to multivalent binding to ...Engineered immunoglobulin M (IgM) antibodies typically exhibit superior neutralization potency and avidity compared to their parental IgG counterparts, primarily due to multivalent binding to repeated epitopes on a targeting antigen. In this study, we characterize the neutralization breadth and mechanism of action of IgM-14, a previously reported intranasally deliverable antibody targeting SARS-CoV-2. IgM-14 demonstrates remarkably potent antiviral activity against all pre-Omicron variants but significantly reduced efficacy against Omicron BA.1, and complete loss of activity against the later subvariant JN.1. Resistance selection identified two key mutations in the receptor-binding domain (RBD), G476D and F486P, which disrupt IgM-14 binding and confer strong resistance. Cryo-electron microscopy analysis uncovered two distinct Fab-RBD interfaces: a primary interface overlapping the angiotensin-converting enzyme 2 (ACE2)-binding region, and a unique secondary interface formed only when the RBD adopts the ACE2-inaccessible "down" conformation, involving a neighboring spike protomer. Site-directed mutagenesis and structural modeling revealed a critical role of this secondary site in IgM-14-mediated neutralization. Unlike IgG-14, structural modeling suggested that IgM-14 can simultaneously engage both interfaces in diverse modes, indicating a noncanonical avidity mechanism. Collectively, these findings highlight the structural and functional uniqueness of IgM-14 and offer valuable insights into the rational design of next-generation spike-targeted antibody therapeutics with enhanced breadth and potency.
History
DepositionOct 13, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73273.png

Downloads & links

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Map

FileDownload / File: emd_73273.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 440 pix.
= 369.116 Å		0.84 Å/pix.
x 440 pix.
= 369.116 Å		0.84 Å/pix.
x 440 pix.
= 369.116 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8389 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3737256 - 0.95067275
Average (Standard dev.)-0.0004832128 (±0.020283353)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 369.11603 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_73273_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Half map: half map B

Fileemd_73273_half_map_2.map
Annotationhalf map B
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AxesZYX

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Sample components

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Entire : SARS-CoV-2 Omicron BA.1 spike

EntireName: SARS-CoV-2 Omicron BA.1 spike
Components
  • Complex: SARS-CoV-2 Omicron BA.1 spike

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Supramolecule #1: SARS-CoV-2 Omicron BA.1 spike

SupramoleculeName: SARS-CoV-2 Omicron BA.1 spike / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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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: 8
GridModel: Quantifoil R2/2 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 43.27 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 10500
Experimental equipment
Model: Titan Krios / 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: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 339659
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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