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- EMDB-39179: Negative stain EM map of SARS-CoV-2 6P spike protein complexed wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-39179
TitleNegative stain EM map of SARS-CoV-2 6P spike protein complexed with polyclonal Fabs isolated from sera of DNA(S)-S-S vaccinated mouse-1
Map dataNegative stain EM map of SARS-CoV-2 6P spike protein complexed with polyclonal Fabs isolated from sera of DNA(S)-S-S vaccinated mouse
Sample
  • Complex: Complex of SARS-CoV-2 6P spike protein with polyclonal Fabs isolated from the sera of DNA(S)-S-S vaccinated mice
    • Complex: Severe acute respiratory syndrome coronavirus-2 6P
    • Complex: polyclonal Fabs isolated from sera of DNA(S)-S-S vaccinated mouse
KeywordsSARS-CoV-2 / Polyclonal antibodies / Complex / VIRAL PROTEIN / PROTEIN BINDING
Biological speciesSevere acute respiratory syndrome coronavirus 2 / Mus musculus (house mouse)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsChen K / Zhu JY
Funding support2 items
OrganizationGrant numberCountry
Other government2022YFA1206400
Other governmentgrant nos. 22277017
CitationJournal: To Be Published
Title: DNA Prime-Protein Boost Targeting Conformational Non-RBD Region for Broad Cross-Neutralization
Authors: Ma YF / Chen K / Xie BW / Zhu JY
History
DepositionFeb 20, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39179.png

Downloads & links

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Map

FileDownload / File: emd_39179.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of SARS-CoV-2 6P spike protein complexed with polyclonal Fabs isolated from sera of DNA(S)-S-S vaccinated mouse
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: 0.0125
Minimum - Maximum-0.0259529 - 0.075457804
Average (Standard dev.)0.0003081068 (±0.004113856)
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: Negative stain EM half map of SARS-CoV-2 6P...

Fileemd_39179_half_map_1.map
AnnotationNegative stain EM half map of SARS-CoV-2 6P spike protein complexed with polyclonal Fabs isolated from sera of DNA(S)-S-S vaccinated mouse
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain EM half map of SARS-CoV-2 6P...

Fileemd_39179_half_map_2.map
AnnotationNegative stain EM half map of SARS-CoV-2 6P spike protein complexed with polyclonal Fabs isolated from sera of DNA(S)-S-S vaccinated mouse
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of SARS-CoV-2 6P spike protein with polyclonal Fabs isola...

EntireName: Complex of SARS-CoV-2 6P spike protein with polyclonal Fabs isolated from the sera of DNA(S)-S-S vaccinated mice
Components
  • Complex: Complex of SARS-CoV-2 6P spike protein with polyclonal Fabs isolated from the sera of DNA(S)-S-S vaccinated mice
    • Complex: Severe acute respiratory syndrome coronavirus-2 6P
    • Complex: polyclonal Fabs isolated from sera of DNA(S)-S-S vaccinated mouse

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Supramolecule #1: Complex of SARS-CoV-2 6P spike protein with polyclonal Fabs isola...

SupramoleculeName: Complex of SARS-CoV-2 6P spike protein with polyclonal Fabs isolated from the sera of DNA(S)-S-S vaccinated mice
type: complex / ID: 1 / Parent: 0
Details: SARS-CoV-2 6P spike protein complexed with polyclonal Fabs isolated from sera of DNA(S)-S-S vaccinated mouse
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2

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Supramolecule #2: Severe acute respiratory syndrome coronavirus-2 6P

SupramoleculeName: Severe acute respiratory syndrome coronavirus-2 6P / type: complex / ID: 2 / Parent: 1 / Details: SARS-CoV-2 6P
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: polyclonal Fabs isolated from sera of DNA(S)-S-S vaccinated mouse

SupramoleculeName: polyclonal Fabs isolated from sera of DNA(S)-S-S vaccinated mouse
type: complex / ID: 3 / Parent: 1
Details: polyclonal Fabs isolated from sera of DNA(S)-S-S vaccinated mouse

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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

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

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xr8

Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 9656
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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