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- EMDB-49324: Polyclonal immune complex of Fab from serum of animal 6 at week 3... -

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Basic information

Entry
Database: EMDB / ID: EMD-49324
TitlePolyclonal immune complex of Fab from serum of animal 6 at week 35 binding H1 HA
Map dataNegative stain map of global refinement of particle stack used to sort polyclonal responses to H1 HA (A/California/04/2009 H1 (HA2 E47K)) from animal 6 week 35
Sample
  • Complex: Polyclonal immune complex of Fab from serum of animal 6 at week 35 binding H1 HA
    • Complex: Fab
    • Complex: hemagglutinin
Keywordsinfluenza virus / hemagglutinin / polyclonal antibody / VIRAL PROTEIN
Biological speciesMacaca mulatta (Rhesus monkey) / Influenza A virus
Methodsingle particle reconstruction / negative staining / Resolution: 30.0 Å
AuthorsHan J / Leon AN / Richey ST / Ferguson JA / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Other government75N93019C00051 United States
CitationJournal: Nat Immunol / Year: 2025
Title: Influenza vaccine based on AS03-adjuvanted chimeric HA induces long-lived stalk-specific plasma cells in bone marrow and lymph nodes of nonhuman primates.
Authors: Akil Akhtar / Tiffany M Styles / Chunyang Gu / André Nicolás León / Gregory K Tharp / Kasey Stokdyk / Anass Abbad / Cora Hirst / Shirin Strohmeier / Gabriele Neumann / Sara T Richey / ...Authors: Akil Akhtar / Tiffany M Styles / Chunyang Gu / André Nicolás León / Gregory K Tharp / Kasey Stokdyk / Anass Abbad / Cora Hirst / Shirin Strohmeier / Gabriele Neumann / Sara T Richey / James A Ferguson / Uchurappa Mala / Hasan Ahmed / Julianna Han / Juan Manuel Carreño / Carl W Davis / Rustom Antia / Peter Palese / Andrew B Ward / Yoshihiro Kawaoka / Florian Krammer / Rafi Ahmed / Rama R Amara /
Abstract: Current influenza vaccines face challenges due to antigenic evolution of the circulating virus and waning immunity in humans. Here we investigated the durability of humoral immunity induced by an ...Current influenza vaccines face challenges due to antigenic evolution of the circulating virus and waning immunity in humans. Here we investigated the durability of humoral immunity induced by an influenza vaccine based on AS03-adjuvanted chimeric hemagglutinin (cHA) in nonhuman primates (NHPs). Two groups of NHPs received two doses of a seasonal quadrivalent influenza vaccine, followed by sequential immunization with split virus cHA vaccines cH8/1N1, and cH5/1N1. One group received cHA immunizations with AS03 adjuvant. We monitored serum antibodies and long-lived plasma cells in bone marrow for nearly 2 years after the final vaccination. cHA vaccines induced stalk-specific antibody responses. The addition of AS03 enhanced both the magnitude and durability of humoral immunity by establishing long-lived plasma cells in the bone marrow and lymph nodes for nearly 2 years. Passive transfer of NHP serum provided protection against challenge with heterologous influenza A virus strains in mice. This study highlights the potential of the AS03-adjuvanted chimeric HA vaccine strategy to provide durable and broadly protective humoral immunity.
History
DepositionFeb 19, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49324.png

Downloads & links

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Map

FileDownload / File: emd_49324.map.gz / Format: CCP4 / Size: 34.3 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 (A/California/04/2009 H1 (HA2 E47K)) from animal 6 week 35
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 208 pix.
= 347.36 Å		1.67 Å/pix.
x 208 pix.
= 347.36 Å		1.67 Å/pix.
x 208 pix.
= 347.36 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: 0.0193
Minimum - Maximum-0.018001214 - 0.078486815
Average (Standard dev.)0.0001433675 (±0.002993122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 347.36 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_49324_additional_1.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA low stem epitope from animal 6 week 35
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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

Fileemd_49324_additional_2.map
AnnotationNegative stain map of polyclonal Fab binding the H1 HA central stem and angled stem epitopes from animal 6 week 35
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_49324_half_map_1.map
AnnotationNegative stain half map B of global refinement of particle stack used to sort polyclonal responses to H1 HA (A/California/04/2009 H1 (HA2 E47K)) from animal 6 week 35
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_49324_half_map_2.map
AnnotationNegative stain half map A of global refinement of particle stack used to sort polyclonal responses to H1 HA (A/California/04/2009 H1 (HA2 E47K)) from animal 6 week 35
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 serum of animal 6 at week 3...

EntireName: Polyclonal immune complex of Fab from serum of animal 6 at week 35 binding H1 HA
Components
  • Complex: Polyclonal immune complex of Fab from serum of animal 6 at week 35 binding H1 HA
    • Complex: Fab
    • Complex: hemagglutinin

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Supramolecule #1: Polyclonal immune complex of Fab from serum of animal 6 at week 3...

SupramoleculeName: Polyclonal immune complex of Fab from serum of animal 6 at week 35 binding H1 HA
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 280 KDa

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Supramolecule #2: Fab

SupramoleculeName: Fab / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #3: hemagglutinin

SupramoleculeName: hemagglutinin / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Influenza A virus / Strain: A/California/04/2009 E47K

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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 20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 73000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4m4y


Details: 30A map generated in Chimera and used as starting model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 70000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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