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- EMDB-71421: KL-H15-6G8 Fab in complex with soluble A/wedge-tailed shearwater/... -

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Basic information

Entry
Database: EMDB / ID: EMD-71421
TitleKL-H15-6G8 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
Map datasharpened map
Sample
  • Complex: KL-H15-6G8 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: KL-15-6G8 heavy chain Fv
    • Protein or peptide: KL-15-6G8 light chain Fv
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza virus / hemagglutinin / avian influenza virus / antibody Fab complex / glycoprotein / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus (A/shearwater/West Australia/2576/79(H15N9)) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.41 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_71421.png

Downloads & links

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Map

FileDownload / File: emd_71421.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.032981176 - 0.053025313
Average (Standard dev.)0.0000068705576 (±0.0013116553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71421_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_71421_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_71421_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : KL-H15-6G8 Fab in complex with soluble A/wedge-tailed shearwater/...

EntireName: KL-H15-6G8 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
Components
  • Complex: KL-H15-6G8 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
    • Protein or peptide: KL-15-6G8 heavy chain Fv
    • Protein or peptide: KL-15-6G8 light chain Fv
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: KL-H15-6G8 Fab in complex with soluble A/wedge-tailed shearwater/...

SupramoleculeName: KL-H15-6G8 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-#4
Source (natural)Organism: Influenza A virus (A/shearwater/West Australia/2576/79(H15N9))

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Macromolecule #1: Hemagglutinin HA1

MacromoleculeName: Hemagglutinin HA1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/shearwater/West Australia/2576/79(H15N9))
Molecular weightTheoretical: 35.870426 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DKICLGHHAV ANGTKVNTLT ERGVEVVNAT ETVEITGIDK VCTKGKKAVD LGSCGILGTI IGPPQCDLHL EFKADLIIER RNSSDICYP GRFTNEEALR QIIRESGGID KESMGFRYSG IRTDGATSAC KRTVSSFYSE MKWLSSSMNN QVFPQLNQTY R NTRKEPAL ...String:
DKICLGHHAV ANGTKVNTLT ERGVEVVNAT ETVEITGIDK VCTKGKKAVD LGSCGILGTI IGPPQCDLHL EFKADLIIER RNSSDICYP GRFTNEEALR QIIRESGGID KESMGFRYSG IRTDGATSAC KRTVSSFYSE MKWLSSSMNN QVFPQLNQTY R NTRKEPAL IVWGVHHSSS LDEQNKLYGT GNKLITVGSS KYQQSFSPSP GARPKVNGQA GRIDFHWMLL DPGDTVTFTF NG AFIAPDR ATFLRSNAPS GIEYNGKSLG IQSDAQIDES CEGECFYSGG TINSPLPFQN IDSRAVGKCP RYVKQSSLPL ALG MKNVPE KI

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2

MacromoleculeName: Hemagglutinin HA2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/shearwater/West Australia/2576/79(H15N9))
Molecular weightTheoretical: 19.678582 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GAIAGFIENG WEGLIDGWYG FRHQNAQGQG TAADYKSTQA AIDQITGKLN RLIEKTNKQF ELIDNEFTEV EQQIGNVINW TRDSLTEIW SYNAELLVAM ENQHTIDLAD SEMNKLYERV RRQLRENAEE DGTGCFEIFH RCDDQCMESI RNNTYNHTEY R QEALQNRI M

UniProtKB: Hemagglutinin

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Macromolecule #3: KL-15-6G8 heavy chain Fv

MacromoleculeName: KL-15-6G8 heavy chain Fv / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.064368 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
EVQLQQCGSL LARPGASVKM SGKASGYSFT IYWMHWVKQR PGQGLEWIGA IYPGNSDASN NQKFTGKANL TAVTSASTAY MELSSLTNE DSAVYYCTRG DYDGYYFDYW GQGTTLTVSS

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Macromolecule #4: KL-15-6G8 light chain Fv

MacromoleculeName: KL-15-6G8 light chain Fv / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.10245 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DIVLTQSPAS LAVSLGQRAT ISCRASQSVS SSTYSYMHLY QQKPGQPPKL LIKYASNLES GVPARFSGSG SGTDFTLNIH PVEEEDTAT YYCQQSWEIP WTFGGGTKLE IK

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 16 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.75 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: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 2346 / Average exposure time: 2.2 sec. / Average electron dose: 50.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 419900
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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