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- EMDB-43888: Negative stain EM map of SARS-COV-2 (XBB) spike protein in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-43888
TitleNegative stain EM map of SARS-COV-2 (XBB) spike protein in complex with Fab COV2-4094
Map data
Sample
  • Complex: SARS-COV-2 (XBB) spike in complex with Fab COV2-3872
    • Complex: Cov2-spike
    • Complex: Fab
KeywordsVIRAL-PROTEIN / Fab / IMMUNE-complex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 18.0 Å
AuthorsBinshtein E / Crowe JE
Funding support United States, 1 items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA)HR0011-18-2-0001 United States
CitationJournal: Nat Microbiol / Year: 2026
Title: Epitope-focused discovery of SARS-CoV-2 antibodies that potently neutralize Omicron variants.
Authors: Seth J Zost / Naveenchandra Suryadevara / Lauren E Williamson / Suzanne M Scheaffer / Elad Binshtein / Cameron D Buchman / Nicole V Johnson / Nicholas J Catanzaro / Silvia Ravera / Nathaniel ...Authors: Seth J Zost / Naveenchandra Suryadevara / Lauren E Williamson / Suzanne M Scheaffer / Elad Binshtein / Cameron D Buchman / Nicole V Johnson / Nicholas J Catanzaro / Silvia Ravera / Nathaniel S Chapman / Luke Myers / Ajit R Ramamohan / Laura S Handal / Doan C Nguyen / Andrew Trivette / James R Martinez / Eduardo Villalobos / Stacey A Rutherford / F Eun-Hyung Lee / Alexandra Schäfer / Ralph S Baric / Jason S McLellan / Michael S Diamond / Robert H Carnahan / James E Crowe /
Abstract: The emergence of SARS-CoV-2 Omicron variants has led to viral escape from many clinically approved monoclonal antibodies (mAbs) due to rapid evolution of the receptor-binding domain (RBD). Co- ...The emergence of SARS-CoV-2 Omicron variants has led to viral escape from many clinically approved monoclonal antibodies (mAbs) due to rapid evolution of the receptor-binding domain (RBD). Co-circulation of SARS-CoV-2 variants with unique sets of antigenic substitutions has further complicated therapeutic mAb discovery. New approaches are needed to rapidly discover and characterize mAbs with preferred specificity and functional characteristics. Here we describe and perform epitope-focused mAb discovery using glycan-masked antigens. We isolated and expressed a panel of 303 mAbs, some of which potently neutralize divergent Omicron subvariants by targeting the class 3 antigenic site on SARS-CoV-2 RBD. Epitope mapping of these antibodies revealed a spectrum of cross-reactivity and differential recognition of the class 3 site, validating the utility of this enrichment approach for targeted mAb discovery. Together, this work rationally designs glycan-masked engineered RBDs and uses them to isolate mAbs that potently neutralize antigenically divergent SARS-CoV-2 variants.
History
DepositionFeb 29, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43888.png

Downloads & links

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Map

FileDownload / File: emd_43888.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.36 Å/pix.
x 128 pix.
= 558.08 Å		4.36 Å/pix.
x 128 pix.
= 558.08 Å		4.36 Å/pix.
x 128 pix.
= 558.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-5.2474403 - 12.275021000000001
Average (Standard dev.)-0.08044448 (±0.53323686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 558.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43888_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_43888_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 : SARS-COV-2 (XBB) spike in complex with Fab COV2-3872

EntireName: SARS-COV-2 (XBB) spike in complex with Fab COV2-3872
Components
  • Complex: SARS-COV-2 (XBB) spike in complex with Fab COV2-3872
    • Complex: Cov2-spike
    • Complex: Fab

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Supramolecule #1: SARS-COV-2 (XBB) spike in complex with Fab COV2-3872

SupramoleculeName: SARS-COV-2 (XBB) spike in complex with Fab COV2-3872 / type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 540 MDa

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Supramolecule #2: Cov2-spike

SupramoleculeName: Cov2-spike / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Fab

SupramoleculeName: Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50 KDa

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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

Concentration0.01 mg/mL
BufferpH: 8
StainingType: NEGATIVE / Material: uranyl formate
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 222 / Average exposure time: 1.0 sec. / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC / Number images used: 14240
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL

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