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- EMDB-43886: Negative stain EM map of SARS-COV-2 (XBB) spike protein in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-43886
TitleNegative stain EM map of SARS-COV-2 (XBB) spike protein in complex with Fab COV2-3906
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: 25.0 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: To Be Published
Title: Negative stain EM map of SARS-COV-2 (XBB) spike protein in complex with Fab COV2-3906
Authors: Binshtein E / Crowe JE
History
DepositionFeb 29, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43886.png

Downloads & links

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Map

FileDownload / File: emd_43886.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: 3.5
Minimum - Maximum-4.2793937 - 12.202199
Average (Standard dev.)-0.09216274 (±0.46876705)
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_43886_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_43886_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: 146 / 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

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC / Number images used: 6742
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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