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- EMDB-44664: Representative polyclonal epitopes targeted on CoV HKU1 spike pro... -

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Basic information

Entry
Database: EMDB / ID: EMD-44664
TitleRepresentative polyclonal epitopes targeted on CoV HKU1 spike protein with complexing by mEM
Map data3D refined map of CoV spike HKU1 with donor 2323 polyclonal antibodies bound to CTD by mEM (C1 symmetry)
Sample
  • Complex: Coronavirus HKU1 spike in complex with polyclonal antibodies from human sera by mEM
KeywordsCoV / spike / HKU1 / polyclonal antibody / complex / microfluidics / VIRAL PROTEIN
Biological speciesHuman coronavirus HKU1
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsSewall LM / Ward AB / Torrents de la Pena A
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI136621 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Nat Biomed Eng / Year: 2025
Title: Rapid and High-Throughput Imaging of Immune Complexes Using Microfluidics and Single Particle Electron Microscopy
Authors: Sewall LM / de Paiva Froes Rocha R / Gibson G / Louie M / Xie Z / Bangaru S / Tran AS / Ozorowski G / Mohanty S / Beutler N / Burton DR / Shaw AC / Batista FD / Chocarro Ruiz B / Torrents de la Pena A / Ward AB
History
DepositionApr 30, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateApr 23, 2025-
Current statusApr 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44664.png

Downloads & links

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Map

FileDownload / File: emd_44664.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D refined map of CoV spike HKU1 with donor 2323 polyclonal antibodies bound to CTD by mEM (C1 symmetry)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 256 pix.
= 427.52 Å		1.67 Å/pix.
x 256 pix.
= 427.52 Å		1.67 Å/pix.
x 256 pix.
= 427.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.028387384 - 0.051640496
Average (Standard dev.)0.00015456672 (±0.0029782115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 427.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3D map of CoV spike HKU1 with donor...

Fileemd_44664_additional_1.map
Annotation3D map of CoV spike HKU1 with donor 2323 polyclonal antibodies bound to NTD and S2 by mEM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D map of CoV spike HKU1 with donor...

Fileemd_44664_additional_2.map
Annotation3D map of CoV spike HKU1 with donor 2333 polyclonal antibody bound to SD2 by mEM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_44664_additional_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D refined half map 2 of CoV spike...

Fileemd_44664_half_map_1.map
Annotation3D refined half map 2 of CoV spike HKU1 with donor 2323 polyclonal antibodies bound to CTD by mEM (C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: 3D refined half map 1 of CoV spike...

Fileemd_44664_half_map_2.map
Annotation3D refined half map 1 of CoV spike HKU1 with donor 2323 polyclonal antibodies bound to CTD by mEM (C1 symmetry)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Coronavirus HKU1 spike in complex with polyclonal antibodies from...

EntireName: Coronavirus HKU1 spike in complex with polyclonal antibodies from human sera by mEM
Components
  • Complex: Coronavirus HKU1 spike in complex with polyclonal antibodies from human sera by mEM

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Supramolecule #1: Coronavirus HKU1 spike in complex with polyclonal antibodies from...

SupramoleculeName: Coronavirus HKU1 spike in complex with polyclonal antibodies from human sera by mEM
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human coronavirus HKU1

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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 / Details: 10 mM Tris, 150 mM NaCl
StainingType: NEGATIVE / Material: Uranyl Formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 56000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

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

6ohw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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