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- EMDB-74879: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H83 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-74879
TitleCryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H83
Map data
Sample
  • Complex: Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with H70 FAB
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Fab H83 Heavy Chain
    • Protein or peptide: Fab H83 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsH5N1 / antibody / influenza / VIRAL PROTEIN / ANTIMICROBIAL 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 speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsMorano NC / Ho DD / Shapiro L / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Biorxiv / Year: 2026
Title: A Panel of Human Monoclonal Antibodies for Tracking the Antigenic Evolution of Influenza H5N1 Clade 2.3.4.4b
Authors: Hong H / Morano NC / Wu M / Chong S / Yu J / Huang Y / Nair MS / Li Z / Tzang CC / Becker JE / Wang C / Shapiro L / Kwong PD / Guo Y / Ho DD
History
DepositionDec 30, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74879.png

Downloads & links

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Map

FileDownload / File: emd_74879.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 495. Å		0.83 Å/pix.
x 600 pix.
= 495. Å		0.83 Å/pix.
x 600 pix.
= 495. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0823
Minimum - Maximum-0.4353515 - 0.69784504
Average (Standard dev.)-0.000045428806 (±0.011748483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 495.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_74879_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74879_half_map_2.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 : Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with H70 FAB

EntireName: Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with H70 FAB
Components
  • Complex: Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with H70 FAB
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Fab H83 Heavy Chain
    • Protein or peptide: Fab H83 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with H70 FAB

SupramoleculeName: Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with H70 FAB
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 65.58575 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENIVLLLAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCDL NGVKPLILKD CSVAGWLLGN PMCDEFIRV PEWSYIVERA NPANDLCYPG SLNDYEELKH MLSRINHFEK IQIIPKSSWP NHETSLGVSA ACPYQGAPSF F RNVVWLIK ...String:
MENIVLLLAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCDL NGVKPLILKD CSVAGWLLGN PMCDEFIRV PEWSYIVERA NPANDLCYPG SLNDYEELKH MLSRINHFEK IQIIPKSSWP NHETSLGVSA ACPYQGAPSF F RNVVWLIK KNDAYPTIKI SYNNTNREDL LILWGIHHSN NAEEQTNLYK NPITYISVGT STLNQRLAPK IATRSQVNGQ RG RMDFFWT ILKPDDAIHF ESNGNFIAPE YAYKIVKKGD STIMKSGVEY GHCNTKCQTP VGAINSSMPF HNIHPLTIGE CPK YVKSNK LVLATGLRNS PLRRRRRRGL FGAIAGFIEG GWQGMVDGWY GYHHSNEQGS GYAADKESTQ KAIDGVTNKV NSII DKMNT QFEAVGREFN NLERRIENLN KKMEDGFLDV WTYNAELLVL MENERTLDFH DSNVKNLYDK VRLQLRDNAK ELGNG CFEF YHKCDNECME SVRNGTYDYP QYSEEARLKR EGSSGSSGYI PEAPRDGQAY VRKDGEWVLL STFLGHHHHH HHHHGG SGL NDIFEAQKIE WHE

UniProtKB: Hemagglutinin

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Macromolecule #2: Fab H83 Heavy Chain

MacromoleculeName: Fab H83 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.085564 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ EQLVESGGGV VQPGRSLRLS CTASGFTFSS HGMHWVRQAP GKGLEWIAVI WYDGTNKFYG DSVKGRFTI SRDNSKNTLF LQMNSLRAED TAVYYCARDR IQLWLQNYYH AMDVWGQGTT VTVSSASTKG PSVFPLAPSS K STSGGTAA ...String:
MGWSCIILFL VATATGVHSQ EQLVESGGGV VQPGRSLRLS CTASGFTFSS HGMHWVRQAP GKGLEWIAVI WYDGTNKFYG DSVKGRFTI SRDNSKNTLF LQMNSLRAED TAVYYCARDR IQLWLQNYYH AMDVWGQGTT VTVSSASTKG PSVFPLAPSS K STSGGTAA LGCLVKDYFP EPVTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DK TVEPKSC DKTHHHHHHH H

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Macromolecule #3: Fab H83 Light Chain

MacromoleculeName: Fab H83 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.432422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSD IQMTQSPSSL SASVGDRVTI TCRASQNIRS YLNWYQQKPG KAPKFLIYGA SSLQSGVPSR FSGSGSGTD FTLTISGLQP EDFATYYCQQ SYTTLPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW ...String:
MGWSCIILFL VATATGVHSD IQMTQSPSSL SASVGDRVTI TCRASQNIRS YLNWYQQKPG KAPKFLIYGA SSLQSGVPSR FSGSGSGTD FTLTISGLQP EDFATYYCQQ SYTTLPLTFG GGTKVEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 12 / 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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9ekf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 30300
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9ekf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 30300
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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