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- EMDB-35962: Immune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p... -

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Basic information

Entry
Database: EMDB / ID: EMD-35962
TitleImmune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein added BS3 crosslinker
Map dataImmune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein added BS3 cross-linker
Sample
  • Complex: Omicron BA.1 6p in complex with W328-6H2 Fab
    • Complex: Severe acute respiratory syndrome coronavirus 2 Omicron BA.1 6p
      • Complex: W328-6H2 Fab
KeywordsComplex / Omicron BA.1 6p / antibody / Homo sapiens / RBD / Fab / Cross-linker / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Severe acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsNan XY / Li YJ / Li JY
Funding support1 items
OrganizationGrant numberCountry
Other government22277017
CitationJournal: To Be Published
Title: Immune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein
Authors: Nan XY / Li YJ / Li JY
History
DepositionApr 17, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateDec 18, 2024-
Current statusDec 18, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35962.png

Downloads & links

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Map

FileDownload / File: emd_35962.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationImmune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein added BS3 cross-linker
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.21 Å/pix.
x 192 pix.
= 424.32 Å		2.21 Å/pix.
x 192 pix.
= 424.32 Å		2.21 Å/pix.
x 192 pix.
= 424.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0227
Minimum - Maximum-0.025498219 - 0.08399581
Average (Standard dev.)0.00018370413 (±0.0049117645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 424.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Immune complex of W328-6H2 Fab binding the RBD...

Fileemd_35962_half_map_1.map
AnnotationImmune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein added BS3 cross-linker
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Immune complex of W328-6H2 Fab binding the RBD...

Fileemd_35962_half_map_2.map
AnnotationImmune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein added BS3 cross-linker
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Omicron BA.1 6p in complex with W328-6H2 Fab

EntireName: Omicron BA.1 6p in complex with W328-6H2 Fab
Components
  • Complex: Omicron BA.1 6p in complex with W328-6H2 Fab
    • Complex: Severe acute respiratory syndrome coronavirus 2 Omicron BA.1 6p
      • Complex: W328-6H2 Fab

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Supramolecule #1: Omicron BA.1 6p in complex with W328-6H2 Fab

SupramoleculeName: Omicron BA.1 6p in complex with W328-6H2 Fab / type: complex / ID: 1 / Parent: 0
Details: Immune complex of W328-6H2 Fab binding the RBD of Omicron BA.1 6p spike protein added BS3 cross-linker
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Severe acute respiratory syndrome coronavirus 2 Omicron BA.1 6p

SupramoleculeName: Severe acute respiratory syndrome coronavirus 2 Omicron BA.1 6p
type: complex / ID: 2 / Parent: 1 / Details: Omicron BA.1 6p
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #3: W328-6H2 Fab

SupramoleculeName: W328-6H2 Fab / type: complex / ID: 3 / Parent: 2 / Details: W328-6H2 Fab
Source (natural)Organism: Homo sapiens (human)

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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

Concentration0.015 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl Acetate

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Electron microscopy

MicroscopeJEOL 2100F
Image recordingFilm or detector model: OTHER / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.5 µm

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 7266
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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