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- EMDB-61616: Cryo-EM structure of a human-infecting bovine influenza H5N1 hema... -

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Basic information

Entry
Database: EMDB / ID: EMD-61616
TitleCryo-EM structure of a human-infecting bovine influenza H5N1 hemagglutinin complexed with avian receptor analog LSTa
Map data
Sample
  • Complex: Human-infecting bovine influenza H5N1 hemagglutinin complexed with avian receptor analog LSTa
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: N-acetyl-alpha-neuraminic acid
Keywordscomplex / VIRAL PROTEIN
Biological speciesInfluenza A virus (A/Indonesia/5/2005(H5N1))
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsWang HC / Han P / Song H / Gao GF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Cell / Year: 2025
Title: Receptor binding, structure, and tissue tropism of cattle-infecting H5N1 avian influenza virus hemagglutinin.
Authors: Hao Song / Tianjiao Hao / Pu Han / Haichen Wang / Xu Zhang / Xiaomei Li / Yuxuan Wang / Jiamin Chen / Ying Li / Xiyue Jin / Xuefeng Duan / Wei Zhang / Yuhai Bi / Ronghua Jin / Lei Sun / ...Authors: Hao Song / Tianjiao Hao / Pu Han / Haichen Wang / Xu Zhang / Xiaomei Li / Yuxuan Wang / Jiamin Chen / Ying Li / Xiyue Jin / Xuefeng Duan / Wei Zhang / Yuhai Bi / Ronghua Jin / Lei Sun / Ningli Wang / George F Gao /
Abstract: The ongoing circulation of highly pathogenic avian influenza (HPAI) A (H5N1) viruses, particularly clade 2.3.4.4b strains, poses a significant threat to animal and public health. Recent outbreaks in ...The ongoing circulation of highly pathogenic avian influenza (HPAI) A (H5N1) viruses, particularly clade 2.3.4.4b strains, poses a significant threat to animal and public health. Recent outbreaks in cattle highlight concerns about cross-species transmission and zoonotic spillover. Here, we found that the hemagglutinin (HA) protein from a cattle-infecting H5N1 virus has acquired slight binding to human-like α2-6-linked receptors while still exhibiting a strong preference for avian-like α2-3-linked sialic acid receptors. Immunohistochemical staining revealed HA binding to bovine pulmonary and mammary tissues, aligning with clinical observations. HA also binds effectively to human conjunctival, tracheal, and mammary tissues, indicating a risk for human transmission, notably in cases of conjunctivitis. High-resolution cryo-electron microscopy (cryo-EM) structures of this H5 HA in complex with either α2-3 or α2-6 receptors elucidate the molecular mechanisms underlying its receptor-binding properties. These findings provide critical insights into the tropism and transmission potential of this emerging pathogen.
History
DepositionSep 22, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61616.png

Downloads & links

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Map

FileDownload / File: emd_61616.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 360 pix.
= 248.4 Å		0.69 Å/pix.
x 360 pix.
= 248.4 Å		0.69 Å/pix.
x 360 pix.
= 248.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.69 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.19429742 - 0.5992604
Average (Standard dev.)-0.00049829093 (±0.025582872)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 248.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61616_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_61616_half_map_2.map
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Sample components

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Entire : Human-infecting bovine influenza H5N1 hemagglutinin complexed wit...

EntireName: Human-infecting bovine influenza H5N1 hemagglutinin complexed with avian receptor analog LSTa
Components
  • Complex: Human-infecting bovine influenza H5N1 hemagglutinin complexed with avian receptor analog LSTa
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: N-acetyl-alpha-neuraminic acid

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Supramolecule #1: Human-infecting bovine influenza H5N1 hemagglutinin complexed wit...

SupramoleculeName: Human-infecting bovine influenza H5N1 hemagglutinin complexed with avian receptor analog LSTa
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Influenza A virus (A/Indonesia/5/2005(H5N1))

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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 (A/Indonesia/5/2005(H5N1))
Molecular weightTheoretical: 57.704934 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CYPGSLNDYE ELKHMLSRIN HFEKIQIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN ...String:
DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CYPGSLNDYE 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 PLREKR RKRGLFGAIA GFIEGGWQGM VDGWYGYHHS NEQGSGYAAD KESTQKAIDG VTNKVNSIID KMNTQFEAVG REFN NLERR IENLNKKMED GFLDVWTYNA ELLVLMENER TLDFHDSNVK NLYDKVRLQL RDNAKELGNG CFEFYHKCDN ECMES VRNG TYDYPQYSEE ARLKREEISG VK

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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: 9 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #6: N-acetyl-alpha-neuraminic acid

MacromoleculeName: N-acetyl-alpha-neuraminic acid / type: ligand / ID: 6 / Number of copies: 1 / Formula: SIA
Molecular weightTheoretical: 309.27 Da
Chemical component information

ChemComp-SIA:
N-acetyl-alpha-neuraminic acid

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.3000000000000003 µm / Nominal defocus min: 1.0 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 352780
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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