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- EMDB-77343: Cryo-EM global density map of BA.1-S/2130WT/2196-S93Y -

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Basic information

Entry
Database: EMDB / ID: EMD-77343
TitleCryo-EM global density map of BA.1-S/2130WT/2196-S93Y
Map data
Sample
  • Complex: Complex of spike protein of SARS-CoV-2 Omicron BA.1 with 2130WT fab and 2196-S93Y IgG
    • Complex: Spike protein of SARS-CoV-2 Omicron BA.1 variant
    • Complex: 2130WT Fab
    • Complex: 2196-S93Y IgG
KeywordsSARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDu J / Pallesen J
Funding support United States, 2 items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Res Sq / Year: 2026
Title: Structure-Guided Design of Therapeutic Antibodies Targeting SARS-CoV-2 Omicron Variants.
Authors: Jesper Pallesen / Jianqiu Du / Yuanhan Wu / Sukanya Ghosh / Kelly Bayruns / Roopak Sadeesh / David Weiner
Abstract: The ongoing evolution of SARS-CoV-2, particularly the emergence of Omicron subvariants, compromised the effectiveness of many therapeutic antibodies. In this study, we employed a structure-guided ...The ongoing evolution of SARS-CoV-2, particularly the emergence of Omicron subvariants, compromised the effectiveness of many therapeutic antibodies. In this study, we employed a structure-guided computational design strategy to systematically optimize the COV2-2196 antibody for improved neutralization of Omicron variants. Through iterative rounds of computational design and experimental validation, we identified key paratope mutations that restored and enhanced antibody binding and neutralization potency against resistant viral strains. Cryo-EM structural analysis revealed the molecular basis for these improvements, highlighting how targeted modifications can accommodate epitope changes introduced by viral evolution. Our approach demonstrates that effective antibody optimization can be achieved using accessible computational resources, providing a practical framework for rapid therapeutic development. These findings underscore the potential of structure-based design to address challenges posed by viral antigenic drift and support the development of broadly effective antibody therapeutics for emerging infectious diseases.
History
DepositionMay 28, 2026-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77343.png

Downloads & links

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Map

FileDownload / File: emd_77343.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 420 pix.
= 442.68 Å		1.05 Å/pix.
x 420 pix.
= 442.68 Å		1.05 Å/pix.
x 420 pix.
= 442.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.511
Minimum - Maximum-3.2755504 - 5.6692505
Average (Standard dev.)0.00035315764 (±0.07531558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 442.68002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_77343_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_77343_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of spike protein of SARS-CoV-2 Omicron BA.1 with 2130WT f...

EntireName: Complex of spike protein of SARS-CoV-2 Omicron BA.1 with 2130WT fab and 2196-S93Y IgG
Components
  • Complex: Complex of spike protein of SARS-CoV-2 Omicron BA.1 with 2130WT fab and 2196-S93Y IgG
    • Complex: Spike protein of SARS-CoV-2 Omicron BA.1 variant
    • Complex: 2130WT Fab
    • Complex: 2196-S93Y IgG

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Supramolecule #1: Complex of spike protein of SARS-CoV-2 Omicron BA.1 with 2130WT f...

SupramoleculeName: Complex of spike protein of SARS-CoV-2 Omicron BA.1 with 2130WT fab and 2196-S93Y IgG
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron BA.1

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Supramolecule #2: Spike protein of SARS-CoV-2 Omicron BA.1 variant

SupramoleculeName: Spike protein of SARS-CoV-2 Omicron BA.1 variant / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2 / Strain: Omicron BA.1

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Supramolecule #3: 2130WT Fab

SupramoleculeName: 2130WT Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: 2196-S93Y IgG

SupramoleculeName: 2196-S93Y IgG / type: complex / ID: 4 / Parent: 1
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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 243248
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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