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- EMDB-74844: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H51 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-74844
TitleCryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab H51
Map data
Sample
  • Complex: Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with H70 FAB
    • Protein or peptide: H51 Fab Heavy Chain
    • Protein or peptide: H51 Fab Light Chain
    • Protein or peptide: Hemagglutinin
  • 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: 2.7 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 29, 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_74844.png

Downloads & links

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Map

FileDownload / File: emd_74844.map.gz / Format: CCP4 / Size: 216 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 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 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: 0.201
Minimum - Maximum-1.6844343 - 2.1856816
Average (Standard dev.)0.0006555348 (±0.04420792)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_74844_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_74844_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: H51 Fab Heavy Chain
    • Protein or peptide: H51 Fab Light Chain
    • Protein or peptide: Hemagglutinin
  • 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: H51 Fab Heavy Chain

MacromoleculeName: H51 Fab Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.309857 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVQSRAE VKKPGESLKI SCQGSGYRFT NYWIAWVRQM PGKGLEWMGI VYPGDSDVRY SPSFEGQVTI SADKSISTAY LQWSSLKAS DTGVYYCARK DGSGSFPFDF WGQGTLVTVS S

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Macromolecule #2: H51 Fab Light Chain

MacromoleculeName: H51 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.676076 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT VSCRASQNVS GTYLAWYQQK PGQAPSLLIY DASIRAIGTP DRFSGSGFGT DLTLIIRRLE PEDFAVYYC QQYGTSPLTF GGGTKVEIK

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Macromolecule #3: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 3 / 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 #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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

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

9ekf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 183858
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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