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- EMDB-44656: Representative polyclonal epitopes targeted on HA Influenza B pro... -

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Basic information

Entry
Database: EMDB / ID: EMD-44656
TitleRepresentative polyclonal epitopes targeted on HA Influenza B protein with complexing by conventional EMPEM
Map data3D refined map of HA Influenza B with donor 2323 polyclonal antibody bound to esterase by conventional EMPEM (C1 symmetry)
Sample
  • Complex: Hemagglutinin Influenza B in complex with polyclonal antibodies from human sera
KeywordsInfluenza / HA / Influenza B / polyclonal antibody / complex / VIRAL PROTEIN
Biological speciesInfluenza A virus
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_44656.png

Downloads & links

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Map

FileDownload / File: emd_44656.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D refined map of HA Influenza B with donor 2323 polyclonal antibody bound to esterase by conventional EMPEM (C1 symmetry)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 160 pix.
= 329.6 Å		2.06 Å/pix.
x 160 pix.
= 329.6 Å		2.06 Å/pix.
x 160 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.04625741 - 0.11736141
Average (Standard dev.)0.00047182562 (±0.0061809025)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: 3D map of HA Influenza B with donor...

Fileemd_44656_additional_1.map
Annotation3D map of HA Influenza B with donor 2336 polyclonal antibody bound to RBS by conventional EMPEM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D map of HA Influenza B with donor...

Fileemd_44656_additional_2.map
Annotation3D map of HA Influenza B with donor 2336 polyclonal antibody bound to side head by conventional EMPEM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D map of HA Influenza B with donor...

Fileemd_44656_additional_3.map
Annotation3D map of HA Influenza B with donor 2327 polyclonal antibody bound to stem by conventional EMPEM
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 HA Influenza...

Fileemd_44656_half_map_1.map
Annotation3D refined half map 2 of HA Influenza B with donor 2323 polyclonal antibody bound to esterase by conventional EMPEM (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 HA Influenza...

Fileemd_44656_half_map_2.map
Annotation3D refined half map 1 of HA Influenza B with donor 2323 polyclonal antibody bound to esterase by conventional EMPEM (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 : Hemagglutinin Influenza B in complex with polyclonal antibodies f...

EntireName: Hemagglutinin Influenza B in complex with polyclonal antibodies from human sera
Components
  • Complex: Hemagglutinin Influenza B in complex with polyclonal antibodies from human sera

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Supramolecule #1: Hemagglutinin Influenza B in complex with polyclonal antibodies f...

SupramoleculeName: Hemagglutinin Influenza B in complex with polyclonal antibodies from human sera
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Influenza A virus

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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:

4m4y

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 50000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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