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- EMDB-71424: KL-H15-6F6 Fab in complex with soluble A/wedge-tailed shearwater/... -

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Basic information

Entry
Database: EMDB / ID: EMD-71424
TitleKL-H15-6F6 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
Map datasharpened map
Sample
  • Complex: KL-H15-6F6 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
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 / cryo EM / Resolution: 3.34 Å
AuthorsLeon AN / Ferguson JA / 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 24, 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_71424.png

Downloads & links

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Map

FileDownload / File: emd_71424.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å		0.72 Å/pix.
x 512 pix.
= 367.616 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
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Contour LevelBy AUTHOR: 0.00214
Minimum - Maximum-0.02319922 - 0.02746356
Average (Standard dev.)0.000015171551 (±0.00042482742)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 367.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71424_msk_1.map
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Half map: half map A

Fileemd_71424_half_map_1.map
Annotationhalf map A
Projections & Slices
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Half map: half map B

Fileemd_71424_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : KL-H15-6F6 Fab in complex with soluble A/wedge-tailed shearwater/...

EntireName: KL-H15-6F6 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
Components
  • Complex: KL-H15-6F6 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer

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Supramolecule #1: KL-H15-6F6 Fab in complex with soluble A/wedge-tailed shearwater/...

SupramoleculeName: KL-H15-6F6 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.70 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 2985 / Average exposure time: 2.61 sec. / Average electron dose: 45.42 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 20.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio (cryoSPARC)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 166675
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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