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- EMDB-50721: Fab of neutralizing mAb K501SP6 binding to the N-terminal domain ... -

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Basic information

Entry
Database: EMDB / ID: EMD-50721
TitleFab of neutralizing mAb K501SP6 binding to the N-terminal domain of Covid-19 BA.1 Spike protein
Map dataFocused refinement of Fab:epitope interaction
Sample
  • Virus: Alphacoronavirus
KeywordsNeutralizing Antibody / Conserved Epitope / Covid-19 / Spike / VIRAL PROTEIN
Biological speciesAlphacoronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBjoernsson KH / Walker MR / Raghavan SSR / Ward AB / Barfod LK
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: To Be Published
Title: Omicron BA.1 Spike protein with neutralizing NTD specific mAb K501SP6
Authors: Bjoernsson KH / Walker MR / Raghavan SSR / Ward AB / Barfod LK
History
DepositionJun 19, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50721.png

Downloads & links

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Map

FileDownload / File: emd_50721.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement of Fab:epitope interaction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.5427742 - 0.7208383
Average (Standard dev.)-0.000060220176 (±0.008380668)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 367.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of the focused refinement

Fileemd_50721_half_map_1.map
AnnotationHalf map of the focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the focused refinement

Fileemd_50721_half_map_2.map
AnnotationHalf map of the focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Alphacoronavirus

EntireName: Alphacoronavirus
Components
  • Virus: Alphacoronavirus

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Supramolecule #1: Alphacoronavirus

SupramoleculeName: Alphacoronavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Details: Omicron BA.1 spike trimer with Fab fragment of human monoclonal antibody K501SP6 produced with hybridoma technology
NCBI-ID: 693996 / Sci species name: Alphacoronavirus / Sci species strain: Omicron BA.1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No
Host (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

Concentration1.2 mg/mL
BufferpH: 7.5 / Details: TBS, pH 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 195000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 591736
CTF correctionSoftware - Name: cryoSPARC (ver. 4.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7wp9


Details: Homotrimer (spike protein) with Fab region of neutralizing mAb K501SP6
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 87875
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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