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Basic information

Entry
Database: EMDB / ID: EMD-71422
Title07-5G01 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
Map datasharpened map
Sample
  • Complex: 07-5G01 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: 07-5G01 heavy chain Fv
    • Protein or peptide: 05-5G01 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: 3.33 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_71422.png

Downloads & links

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Map

FileReleased
Annotationsharpened map
Voxel sizeX=Y=Z: 0.833 Å
Density
Contour LevelBy AUTHOR: 0.252
Minimum - Maximum-1.450124 - 2.499899
Average (Standard dev.)0.00015408169 (±0.03716669)
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_71422_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 : 07-5G01 Fab in complex with soluble A/wedge-tailed shearwater/Wes...

EntireName: 07-5G01 Fab in complex with soluble A/wedge-tailed shearwater/Western Australia/2576/1979 H15 hemagglutinin trimer
Components
  • Complex: 07-5G01 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: 07-5G01 heavy chain Fv
    • Protein or peptide: 05-5G01 light chain Fv
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: 07-5G01 Fab in complex with soluble A/wedge-tailed shearwater/Wes...

SupramoleculeName: 07-5G01 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: 35.498973 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 MKNVP

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: 07-5G01 heavy chain Fv

MacromoleculeName: 07-5G01 heavy chain Fv / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.448973 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
EVQLVESGGG LVQPGGSLRL SCAASGFTLS TYSMNWVRQA PGKGLEWVSY ISSDSTTIYY ADSVKGRFSI SRDNAKNSLS LQMNSLRAE DTAVFYCARA LTNNKDYFYF MDVWGKGTTV TVSS

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Macromolecule #4: 05-5G01 light chain Fv

MacromoleculeName: 05-5G01 light chain Fv / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.57287 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
EIVLTQSPAT LSLSPGERAT LSCRASQNVS SYLAWYQQKP GQAPRLLIYD AFNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAIYSCQ QRSSWPPTFG GGTKVEIK

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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: 18 / 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: GLOW DISCHARGE
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: 767 / Average electron dose: 49.64 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: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 92304
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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