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- EMDB-71796: Cryo-EM structure of stabilized H5N1 A/Texas/37/2024 hemagglutini... -

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Basic information

Entry
Database: EMDB / ID: EMD-71796
TitleCryo-EM structure of stabilized H5N1 A/Texas/37/2024 hemagglutinin fused to foldon
Map dataCryo-EM structure of stabilized H5N1 A/Texas/37/2024 hemagglutinin fused to foldon
Sample
  • Virus: Influenza A virus
    • Protein or peptide: Hemagglutinin, foldon fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHPAI H5N1 / Influenza Hemagglutinin / stabilization / VIRAL PROTEIN
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDosey A / King N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI181881 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of stabilized H5N1 A/Texas/37/2024 hemagglutinin fused to foldon
Authors: Dosey A / King N
History
DepositionJul 23, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71796.png

Downloads & links

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Map

FileDownload / File: emd_71796.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of stabilized H5N1 A/Texas/37/2024 hemagglutinin fused to foldon
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 400 pix.
= 337.2 Å		0.84 Å/pix.
x 400 pix.
= 337.2 Å		0.84 Å/pix.
x 400 pix.
= 337.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.843 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.5325549 - 0.8036606
Average (Standard dev.)0.0000043582086 (±0.021665672)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 337.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_71796_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map of stabilized H5N1 A/Texas/37/2024 hemagglutinin...

Fileemd_71796_half_map_1.map
AnnotationCryo-EM half map of stabilized H5N1 A/Texas/37/2024 hemagglutinin fused to foldon
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map of stabilized H5N1 A/Texas/37/2024 hemagglutinin...

Fileemd_71796_half_map_2.map
AnnotationCryo-EM half map of stabilized H5N1 A/Texas/37/2024 hemagglutinin fused to foldon
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Influenza A virus

EntireName: Influenza A virus
Components
  • Virus: Influenza A virus
    • Protein or peptide: Hemagglutinin, foldon fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Influenza A virus

SupramoleculeName: Influenza A virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: H5N1 ectodomain recombinantly expressed in HEK293F cells.
NCBI-ID: 11320 / Sci species name: Influenza A virus / Sci species strain: H5N1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Hemagglutinin, foldon fusion

MacromoleculeName: Hemagglutinin, foldon fusion / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Texas/37/2024
Molecular weightTheoretical: 63.09682 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CFPGSLNDYE ELKHMLSRIN HFEKIQIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN ...String:
DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CFPGSLNDYE ELKHMLSRIN HFEKIQIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN REDLLILWGI HHSNNAEEQT NLYKNPITYI SVGTSTLNQR LAPKIATRSQ VNGQRGRMDF FWTILKPDDA IH FESNGNF IAPEYAYKIV KKGDSTIMKS GVEYGHCNTK CQTPVGAINS SMPFHNIHPL TIGECPKYVK SNKLVLATGL RNS PLRESR GLFGAIAGFI EGGWQGMVDG WYGYHFSNEQ GSGYAADKES TQKAIDGVTN MVNSIIDKMN TQFEAVGMEF NNLE RRIEN LNKKMEDGFI DVWTYNAELL VLMLNERTLD FHDSNVKNLY DKVRLQLRDN AKELGNGCFE FYHKCDNECM ESVRN GTYD YPQYSEEARL KREEISGVGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGSG LNDIFEAQKI EWHEGHHHHH H

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 15 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 54035
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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