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- EMDB-60864: Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-60864
TitleCryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex with three-nAb 8H12, 3E2 and 1C4
Map data
Sample
  • Complex: SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4
    • Complex: Spike of BA.1 variant
    • Complex: The Fab fragments of three-nAb 8H12, 3E2 and 1C4
KeywordsCryo-EM / SARs-CoV-2 / antibody / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMus musculus (house mouse) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsSun H / Jiang Y / Li S / Zheng Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of SARS-CoV-2 BA.1 spike protein in complex with three-nAb 8H12, 3E2 and 1C4
Authors: Sun H / Jiang Y / Li S / Zheng Q
History
DepositionJul 20, 2024-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60864.png

Downloads & links

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Map

FileDownload / File: emd_60864.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 576 pix.
= 448.128 Å		0.78 Å/pix.
x 576 pix.
= 448.128 Å		0.78 Å/pix.
x 576 pix.
= 448.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.778 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035
Minimum - Maximum-0.077996716 - 0.25573358
Average (Standard dev.)-0.0003282166 (±0.0070740604)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 448.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60864_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_60864_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 BA.5 spike protein in complex with nAb 1C4

EntireName: SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4
Components
  • Complex: SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4
    • Complex: Spike of BA.1 variant
    • Complex: The Fab fragments of three-nAb 8H12, 3E2 and 1C4

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Supramolecule #1: SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4

SupramoleculeName: SARS-CoV-2 BA.5 spike protein in complex with nAb 1C4 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #2: Spike of BA.1 variant

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

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Supramolecule #3: The Fab fragments of three-nAb 8H12, 3E2 and 1C4

SupramoleculeName: The Fab fragments of three-nAb 8H12, 3E2 and 1C4 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

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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

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / 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: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 286938
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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