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- EMDB-72535: Negative stain map of A/New York/631/1996 H3N2 HA in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-72535
TitleNegative stain map of A/New York/631/1996 H3N2 HA in complex with 88_B4 IgG
Map data
Sample
  • Complex: A/New York/631/1996 H3N2 HA in complex with 88_B4 IgG
KeywordsInfluenza / Hemagglutinin / Antibody complex / Viral protein
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsJo G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93021C00015 United States
CitationJournal: Cell Host Microbe / Year: 2026
Title: Childhood immunological imprinting of cross-subtype antibodies targeting the hemagglutinin head domain of influenza viruses.
Authors: Shuk Hang Li / Bo Wang / Gyunghee Jo / Artem Mikelov / Reilly K Atkinson / Valerie Le Sage / Colleen Furey / Jordan T Ort / Naiqing Ye / Sydney Gang / Ruhi Shah / Jefferson J S Santos / ...Authors: Shuk Hang Li / Bo Wang / Gyunghee Jo / Artem Mikelov / Reilly K Atkinson / Valerie Le Sage / Colleen Furey / Jordan T Ort / Naiqing Ye / Sydney Gang / Ruhi Shah / Jefferson J S Santos / Katharina Röltgen / Shilpa A Joshi / Ji-Yeun Lee / Taylor A Pursell / Elizabeth M Drapeau / Julianna Han / Amy P Callear / Ronald G Collman / Arnold S Monto / Emily T Martin / Seema S Lakdawala / Andrew B Ward / Ian A Wilson / Scott D Boyd / Scott E Hensley /
Abstract: Influenza virus cross-subtype antibodies targeting epitopes in the hemagglutinin (HA) head are rare because these epitopes are variable between influenza virus subtypes. We found that a large ...Influenza virus cross-subtype antibodies targeting epitopes in the hemagglutinin (HA) head are rare because these epitopes are variable between influenza virus subtypes. We found that a large proportion of monoclonal antibodies (mAbs) isolated from individuals immunized with the 2021-22 seasonal influenza vaccine bound to an epitope on the HA head of both the H1N1 vaccine strain and H3N2 strains from the mid-1990s. The unmutated common ancestors of many of these mAbs reacted to both the 1990s H3s and the 2021-22 H1 vaccine strain. These cross-subtype antibodies were also found in polyclonal sera, but only among individuals born in the 1990s. Ferrets sequentially exposed to a 1990s H3N2 virus and contemporary influenza vaccine also produced H1/H3 cross-reactive antibodies. Recently, H1N1 viruses have acquired a substitution that abrogates the binding of these antibodies. Together, our study demonstrates how prior influenza virus exposures can influence the specificity of antibodies elicited by entirely different influenza virus subtypes.
History
DepositionSep 6, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72535.png

Downloads & links

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Map

FileDownload / File: emd_72535.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 180 pix.
= 370.8 Å		2.06 Å/pix.
x 180 pix.
= 370.8 Å		2.06 Å/pix.
x 180 pix.
= 370.8 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: 0.0137
Minimum - Maximum-0.027772177 - 0.046256986
Average (Standard dev.)0.00003904334 (±0.0034878086)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 370.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72535_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72535_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A/New York/631/1996 H3N2 HA in complex with 88_B4 IgG

EntireName: A/New York/631/1996 H3N2 HA in complex with 88_B4 IgG
Components
  • Complex: A/New York/631/1996 H3N2 HA in complex with 88_B4 IgG

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Supramolecule #1: A/New York/631/1996 H3N2 HA in complex with 88_B4 IgG

SupramoleculeName: A/New York/631/1996 H3N2 HA in complex with 88_B4 IgG / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

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

4m4y

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 5307
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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