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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
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: To Be Published
Title: Characterization of the antigenicity of influenza A virus hemagglutinin subtype H15
Authors: Bhavsar D / Leon AN
History
DepositionJun 24, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71421.png

Downloads & links

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Map

FileReleased
Annotationsharpened map
Voxel sizeX=Y=Z: 0.833 Å
Density
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

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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