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- EMDB-45286: Cryo EM map of SARS-COV-2 (BQ 1.1) spike protein in complex with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-45286
TitleCryo EM map of SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891 (2 open 1 close)
Map data
Sample
  • Complex: SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891
    • Complex: SARS-COV-2 (BQ 1.1) spike
    • Complex: Fab COV-3891
KeywordsVIRAL-PROTEIN / Fab / IMMUNE-complex / SARS-CoV-2 / VIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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
DepositionJun 11, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45286.png

Downloads & links

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Map

FileDownload / File: emd_45286.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 400 pix.
= 388.2 Å		0.97 Å/pix.
x 400 pix.
= 388.2 Å		0.97 Å/pix.
x 400 pix.
= 388.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9705 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.032714613 - 0.08250044
Average (Standard dev.)0.00003672955 (±0.0024858734)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 388.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45286_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_45286_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 (BQ 1.1) spike protein in complex with Fab COV2-3891

EntireName: SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891
Components
  • Complex: SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891
    • Complex: SARS-COV-2 (BQ 1.1) spike
    • Complex: Fab COV-3891

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Supramolecule #1: SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891

SupramoleculeName: SARS-COV-2 (BQ 1.1) spike protein in complex with Fab COV2-3891
type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 540 MDa

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Supramolecule #2: SARS-COV-2 (BQ 1.1) spike

SupramoleculeName: SARS-COV-2 (BQ 1.1) spike / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: Fab COV-3891

SupramoleculeName: Fab COV-3891 / 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 14000 / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION, cryoSPARC) / Number images used: 167000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL

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