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- EMDB-44655: Representative polyclonal epitopes targeted on HA H1 protein with... -

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Basic information

Entry
Database: EMDB / ID: EMD-44655
TitleRepresentative polyclonal epitopes targeted on HA H1 protein with complexing by conventional EMPEM
Map data3D refined map of HA H1 with donor 2323 polyclonal antibody bound to RBS by conventional EMPEM (C1 symmetry)
Sample
  • Complex: Hemagglutinin H1 in complex with polyclonal antibodies from human sera.
KeywordsInfluenza / HA / H1 / 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_44655.png

Downloads & links

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Map

FileDownload / File: emd_44655.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D refined map of HA H1 with donor 2323 polyclonal antibody bound to RBS 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-0.036489245 - 0.070410706
Average (Standard dev.)0.00020982657 (±0.0052877576)
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 H1 with donor 2323...

Fileemd_44655_additional_1.map
Annotation3D map of HA H1 with donor 2323 polyclonal antibody bound to esterase 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 H1 with donor 2327...

Fileemd_44655_additional_2.map
Annotation3D map of HA H1 with donor 2327 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 H1 with donor 2323...

Fileemd_44655_additional_3.map
Annotation3D map of HA H1 with donor 2323 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 H1...

Fileemd_44655_half_map_1.map
Annotation3D refined half map 2 of HA H1 with donor 2323 polyclonal antibody bound to RBS 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 H1...

Fileemd_44655_half_map_2.map
Annotation3D refined half map 1 of HA H1 with donor 2323 polyclonal antibody bound to RBS 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 H1 in complex with polyclonal antibodies from human...

EntireName: Hemagglutinin H1 in complex with polyclonal antibodies from human sera.
Components
  • Complex: Hemagglutinin H1 in complex with polyclonal antibodies from human sera.

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Supramolecule #1: Hemagglutinin H1 in complex with polyclonal antibodies from human...

SupramoleculeName: Hemagglutinin H1 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
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.

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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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