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- EMDB-71481: Negative stain map of H15 HA (A/wedge-tailed shearwater/Western A... -

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Basic information

Entry
Database: EMDB / ID: EMD-71481
TitleNegative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Map dataNegative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Sample
  • Complex: Negative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Keywordsinfluenza virus / hemagglutinin / avian influenza virus / antibody Fab complex / glycoprotein / VIRAL PROTEIN
Biological speciesInfluenza A virus (A/shearwater/West Australia/2576/79(H15N9))
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsLeon AN / Bhavsar D / Han JH / 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: Cell Rep / Year: 2026
Title: Structural and functional characterization of the antigenicity of influenza A virus hemagglutinin subtype H15.
Authors: Disha Bhavsar / André Nicolás León / Wei-Li Hsu / Eduard Puente-Massaguer / James A Ferguson / Julianna Han / Patrick Wilson / Andrew B Ward / Florian Krammer /
Abstract: Avian H15 influenza viruses are closely related to H7 viruses, but only 22 H15 sequences have been reported since 1987, suggesting both rarity and minimal antigenic variation. Here, we characterized ...Avian H15 influenza viruses are closely related to H7 viruses, but only 22 H15 sequences have been reported since 1987, suggesting both rarity and minimal antigenic variation. Here, we characterized a panel of mouse monoclonal antibodies (mAbs) raised against the A/wedge-tailed shearwater/Western Australia/2576/1979 ancestral strain, and a human mAb isolated from an H7N9 vaccinee. We found differences in binding and neutralization profiles against the ancestral strain and drifted strains of H15 isolated after 2008. mAbs exhibiting hemagglutination inhibition activity against the ancestral strain do not show binding to drifted strains, hinting at antigenic differences near the receptor binding site. We show that the mAbs protect in vivo and elucidate mAb-antigen interactions using negative stain and cryo-electron microscopy. The characterization of H15 antigenicity and the mechanisms of antibody-mediated neutralization expands our knowledge of this sparsely sampled avian influenza virus subtype and informs our understanding of immune pressures on viral surface glycoproteins.
History
DepositionJun 26, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71481.png

Downloads & links

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Map

FileDownload / File: emd_71481.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
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: 0.0182
Minimum - Maximum-0.039431628 - 0.120415546
Average (Standard dev.)0.000033170243 (±0.005025566)
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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Half map: Negative stain half map A of H15 HA...

Fileemd_71481_half_map_1.map
AnnotationNegative stain half map A of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain half map B of H15 HA...

Fileemd_71481_half_map_2.map
AnnotationNegative stain half map B of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Negative stain map of H15 HA (A/wedge-tailed shearwater/Western A...

EntireName: Negative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Components
  • Complex: Negative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11

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Supramolecule #1: Negative stain map of H15 HA (A/wedge-tailed shearwater/Western A...

SupramoleculeName: Negative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Influenza A virus (A/shearwater/West Australia/2576/79(H15N9))

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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
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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Details: apo negative stain map of A/Hong Kong/4801/2014 H3 generated by depositing lab
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 12700
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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