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- EMDB-47798: Polyclonal immune complex of Fab from pooled Ferret sera at day 2... -

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Entry
Database: EMDB / ID: EMD-47798
TitlePolyclonal immune complex of Fab from pooled Ferret sera at day 28 binding B/Washington HA after infection with B/Washington/02/2019
Map dataNegative stain global refinement of particle stack used to sort polyclonal responses to B/Washington HA from pooled ferret sera at day 28 after infection with B/Washington/02/2019
Sample
  • Complex: Polyclonal immune complex of Fab from pooled Ferret sera at day 28 binding B/Washington HA after infection with B/Washington/02/2019
Keywordsinfluenza / hemagglutinin / Flu B / polyclonal / complex / fab complex / VIRAL PROTEIN
Biological speciesMustela putorius furo (domestic ferret)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsFerguson JA / Rodriguez AJ / Han J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: Sci Adv / Year: 2025
Title: Neuraminidase-specific antibodies drive differential cross-protection between contemporary FLUBV lineages.
Authors: Caroline K Page / Justin D Shepard / Sean D Ray / James A Ferguson / Alesandra J Rodriguez / Julianna Han / Joel C Jacob / Dawne K Rowe-Haas / Jasmine Y Akinpelu / Lilach M Friedman / Tomer ...Authors: Caroline K Page / Justin D Shepard / Sean D Ray / James A Ferguson / Alesandra J Rodriguez / Julianna Han / Joel C Jacob / Dawne K Rowe-Haas / Jasmine Y Akinpelu / Lilach M Friedman / Tomer Hertz / Andrew B Ward / Stephen M Tompkins /
Abstract: The two influenza B virus (FLUBV) lineages have continuously diverged from each other since the 1980s, with recent (post-2015) viruses exhibiting accelerated evolutionary rates. Emerging data from ...The two influenza B virus (FLUBV) lineages have continuously diverged from each other since the 1980s, with recent (post-2015) viruses exhibiting accelerated evolutionary rates. Emerging data from human studies and epidemiological models suggest that increased divergence in contemporary viruses may drive differential cross-protection, where infection with Yamagata lineage viruses provides limited immunity against Victoria lineage viruses. Here, we developed animal models to investigate the mechanisms behind asymmetric cross-protection between contemporary FLUBV lineages. Our results show that contemporary Victoria immunity provides robust cross-protection against the Yamagata lineage, whereas Yamagata immunity offers limited protection against the Victoria lineage. This differential cross-protection is driven by Victoria-elicited neuraminidase (NA)-specific antibodies, which show cross-lineage reactivity, unlike those from Yamagata infections. These findings identify a phenomenon in contemporary FLUBV that may help explain the recent disappearance of the Yamagata lineage from circulation, highlighting the crucial role of targeting NA in vaccination strategies to enhance cross-lineage FLUBV protection.
History
DepositionNov 8, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47798.png

Downloads & links

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Map

FileDownload / File: emd_47798.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain global refinement of particle stack used to sort polyclonal responses to B/Washington HA from pooled ferret sera at day 28 after infection with B/Washington/02/2019
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 208 pix.
= 416. Å		2 Å/pix.
x 208 pix.
= 416. Å		2 Å/pix.
x 208 pix.
= 416. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0168
Minimum - Maximum-0.02361457 - 0.061740194
Average (Standard dev.)0.000094934505 (±0.0028284492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Negative stain map of polyclonal Fab binding the...

Fileemd_47798_additional_1.map
AnnotationNegative stain map of polyclonal Fab binding the B/Washington HA sidehead epitope from pooled ferret sera at day 28 after infection with B/Washington/02/2019
Projections & Slices
AxesZYX

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Additional map: Negative stain map of polyclonal Fab binding the...

Fileemd_47798_additional_2.map
AnnotationNegative stain map of polyclonal Fab binding the B/Washington HA tophead epitope from pooled ferret sera at day 28 after infection with B/Washington/02/2019
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain half map A for global refinement...

Fileemd_47798_half_map_1.map
AnnotationNegative stain half map A for global refinement of particle stack used to sort polyclonal responses to B/Washington HA from pooled ferret sera at day 28 after infection with B/Washington/02/2019
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain half map B for global refinement...

Fileemd_47798_half_map_2.map
AnnotationNegative stain half map B for global refinement of particle stack used to sort polyclonal responses to B/Washington HA from pooled ferret sera at day 28 after infection with B/Washington/02/2019
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Polyclonal immune complex of Fab from pooled Ferret sera at day 2...

EntireName: Polyclonal immune complex of Fab from pooled Ferret sera at day 28 binding B/Washington HA after infection with B/Washington/02/2019
Components
  • Complex: Polyclonal immune complex of Fab from pooled Ferret sera at day 28 binding B/Washington HA after infection with B/Washington/02/2019

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Supramolecule #1: Polyclonal immune complex of Fab from pooled Ferret sera at day 2...

SupramoleculeName: Polyclonal immune complex of Fab from pooled Ferret sera at day 28 binding B/Washington HA after infection with B/Washington/02/2019
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mustela putorius furo (domestic ferret)
Molecular weightTheoretical: 280 KDa

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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: 2% w/v uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeTFS TALOS F200C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

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

4fqm

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 5045
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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