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- EMDB-41563: Polyclonal immune complex of Fab binding the H1 HA from serum of ... -

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Basic information

Entry
Database: EMDB / ID: EMD-41563
TitlePolyclonal immune complex of Fab binding the H1 HA from serum of subject 2-2 at week 16
Map dataNegative stain map of global refinement of particle stack used to sort polyclonal responses to H1 HA from human subject 2-2 at week 16
Sample
  • Complex: Polyclonal immune complex of Fab binding the H1 HA from serum of subject 2-2 at week 16
Keywordsinfluenza / hemagglutinin / H2 / polyclonal complex / Fab complex / viral fusion protein / VIRAL PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsYang YR / Han J / Richey ST / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: bioRxiv / Year: 2023
Title: Immune memory shapes human polyclonal antibody responses to H2N2 vaccination.
Authors: Yuhe R Yang / Julianna Han / Hailee R Perrett / Sara T Richey / Abigail M Jackson / Alesandra J Rodriguez / Rebecca A Gillespie / Sarah O'Connell / Julie E Raab / Lauren Y Cominsky / Ankita ...Authors: Yuhe R Yang / Julianna Han / Hailee R Perrett / Sara T Richey / Abigail M Jackson / Alesandra J Rodriguez / Rebecca A Gillespie / Sarah O'Connell / Julie E Raab / Lauren Y Cominsky / Ankita Chopde / Masaru Kanekiyo / Katherine V Houser / Grace L Chen / Adrian B McDermott / Sarah F Andrews / Andrew B Ward /
Abstract: Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in ...Influenza A virus subtype H2N2, which caused the 1957 influenza pandemic, remains a global threat. A recent phase I clinical trial investigating a ferritin nanoparticle displaying H2 hemagglutinin in H2-naïve and H2-exposed adults. Therefore, we could perform comprehensive structural and biochemical characterization of immune memory on the breadth and diversity of the polyclonal serum antibody response elicited after H2 vaccination. We temporally map the epitopes targeted by serum antibodies after first and second vaccinations and show previous H2 exposure results in higher responses to the variable head domain of hemagglutinin while initial responses in H2-naïve participants are dominated by antibodies targeting conserved epitopes. We use cryo-EM and monoclonal B cell isolation to describe the molecular details of cross-reactive antibodies targeting conserved epitopes on the hemagglutinin head including the receptor binding site and a new site of vulnerability deemed the medial junction. Our findings accentuate the impact of pre-existing influenza exposure on serum antibody responses.
History
DepositionAug 8, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41563.png

Downloads & links

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Map

FileDownload / File: emd_41563.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain map of global refinement of particle stack used to sort polyclonal responses to H1 HA from human subject 2-2 at week 16
Voxel sizeX=Y=Z: 1.77 Å
Density
Contour LevelBy AUTHOR: 0.0205
Minimum - Maximum-0.028578756 - 0.07202905
Average (Standard dev.)0.0001255359 (±0.0044663725)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 318.6 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_41563_additional_1.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA top head 1 epitope from human subject 2-2 at week 16
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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

Fileemd_41563_additional_2.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA central stem epitope from human subject 2-2 at week 16
Projections & Slices
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Additional map: Negative stain map of polyclonal Fab binding the...

Fileemd_41563_additional_3.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA RBS epitope from human subject 2-2 at week 16
Projections & Slices
AxesZYX

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Histogram

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

Fileemd_41563_additional_4.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA medial junction epitope from human subject 2-2 at week 16
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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

Fileemd_41563_additional_5.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA top head 2 epitope from human subject 2-2 at week 16
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_41563_additional_6.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA top head 3 epitope from human subject 2-2 at week 16
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain map of half map A for...

Fileemd_41563_half_map_1.map
AnnotationNegative stain map of half map A for global refinement of particle stack used to sort polyclonal responses to H1 HA from human subject 2-2 at week 16
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain map of half map B for...

Fileemd_41563_half_map_2.map
AnnotationNegative stain map of half map B for global refinement of particle stack used to sort polyclonal responses to H1 HA from human subject 2-2 at week 16
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 binding the H1 HA from serum of ...

EntireName: Polyclonal immune complex of Fab binding the H1 HA from serum of subject 2-2 at week 16
Components
  • Complex: Polyclonal immune complex of Fab binding the H1 HA from serum of subject 2-2 at week 16

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Supramolecule #1: Polyclonal immune complex of Fab binding the H1 HA from serum of ...

SupramoleculeName: Polyclonal immune complex of Fab binding the H1 HA from serum of subject 2-2 at week 16
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
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 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI F20
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: -2.0 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 25.0 e/Å2
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:

3ku5

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 65400

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