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- EMDB-37532: apo toad HA -

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Basic information

Entry
Database: EMDB / ID: EMD-37532
Titleapo toad HA
Map data
Sample
  • Complex: Toad Hemagglutinin
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHemagglutinin / VIRAL PROTEIN
Function / homologyHaemagglutinin, influenzavirus B / Haemagglutinin / Haemagglutinin, influenzavirus A/B / host cell surface receptor binding / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / membrane / Hemagglutinin
Function and homology information
Biological speciesWuhan asiatic toad influenza virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsZhang D / Xie YF / Chai Y / Shi Y / Liu WJ / Qi JX / Gao GF / Gao F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Virol / Year: 2025
Title: Structural basis of receptor-binding adaptation of human-infecting H3N8 influenza A virus.
Authors: Tianjiao Hao / Yufeng Xie / Yan Chai / Wei Zhang / Di Zhang / Jianxun Qi / Yi Shi / Hao Song / George F Gao /
Abstract: Recent avian-origin H3N8 influenza A virus (IAV) that have infected humans pose a potential public health concern. Alterations in the viral surface glycoprotein, hemagglutinin (HA), are typically ...Recent avian-origin H3N8 influenza A virus (IAV) that have infected humans pose a potential public health concern. Alterations in the viral surface glycoprotein, hemagglutinin (HA), are typically required for IAVs to cross the species barrier for adaptation to a new host, but whether H3N8 has adapted to infect humans remains elusive. The observation of a degenerative codon in position 228 of HA in human H3N8 A/Henan/4-10/2022 protein sequence, which could be residue G or S, suggests a dynamic viral adaptation for human infection. Previously, we found this human-isolated virus has shown the ability to transmit between ferrets via respiratory droplets, with the HA-G228S substitution mutation emerging as a critical determinant for the airborne transmission of the virus in ferrets. Here, we investigated the receptor-binding properties of these two H3N8 HAs. Our results showed H3N8 HAs have dual receptor-binding properties with a preference for avian receptor binding, and G228S slightly increased binding to human receptors. Cryo-electron microscopy structures of the two H3N8 HAs with avian and human receptor analogs revealed the basis for dual receptor binding. Mutagenesis studies reveal that the Q226L mutation shifts H3N8 HA's receptor preference from avian to human, while the G228S substitution enhances binding to both receptor types. H3N8 exhibits distinct antigenic sites compared to H3N2, prompting concerns regarding vaccine efficacy. These findings suggest that the current H3N8 human isolates are yet to adapt for efficient human-to-human transmission and further continuous surveillance should be implemented.IMPORTANCEInfluenza virus transmission remains a public health concern currently. H3N8 subtype influenza A viruses infect humans and their HAs acquire the ability to bind to both human and avian receptors, posing a threat to human health. We have solved and analyzed the structural basis of dual receptor binding of recently human-infecting H3N8 HA, and we demonstrate that the G228S enhances human receptor binding and adaptation. We also found that HN/4-10 H3N8 HA has distinct antigenic sites, which challenges vaccine efficacy. Taken together, our work is critical to the prevention and control of human H3 influenza virus infection.
History
DepositionSep 22, 2023-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_37532.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 360 pix.
= 309.6 Å
0.86 Å/pix.
x 360 pix.
= 309.6 Å
0.86 Å/pix.
x 360 pix.
= 309.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 1.84
Minimum - Maximum-11.712576 - 17.095749999999999
Average (Standard dev.)-0.0019871686 (±0.3058855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 309.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_37532_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Half map: #2

Fileemd_37532_half_map_2.map
Projections & Slices
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Sample components

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Entire : Toad Hemagglutinin

EntireName: Toad Hemagglutinin
Components
  • Complex: Toad Hemagglutinin
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Toad Hemagglutinin

SupramoleculeName: Toad Hemagglutinin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Wuhan asiatic toad influenza virus

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Wuhan asiatic toad influenza virus
Molecular weightTheoretical: 54.95159 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NQICIGKAIK PINGTVETVS RMAKVTGMKK VGGERMQKIC AKGEQIHDSS SACGIVSHHL KQEGCDFPFL LNKPKFATTG PMNTSTTGF NFYLTEKAKS WMNITWRVLG ENKDFGDNLV EKYGESGATS EGATLKNYYW YVPTAKPGPV VYEKLAECTG T IYYGALLS ...String:
NQICIGKAIK PINGTVETVS RMAKVTGMKK VGGERMQKIC AKGEQIHDSS SACGIVSHHL KQEGCDFPFL LNKPKFATTG PMNTSTTGF NFYLTEKAKS WMNITWRVLG ENKDFGDNLV EKYGESGATS EGATLKNYYW YVPTAKPGPV VYEKLAECTG T IYYGALLS DAEAGYIAVT GRNVTERWDV RFTGSSESSI SFSGPKQSPM EEYIIKSVRS SVDTVRNIII LDSGRVKKGE TF SISLSSG AVVIPTIFCD GDFAVTPQVQ IDKDCASDCH SAYGSFPNGS SFIIHHSVHT VGSCPPSILR NFDVIDGYEA TWE ETKQSR GFFGAILGFF TGGIQGAIDG WYGVTNHDTG KGTAADQTST QKAVEAITNK LNEAIENGNQ RYNQLYGLAR TQAE LLGNL GKEVNDLRLE TFTEFIRLET ILVNTRIIEE HQAIGSKKKE EVKRLLGPNA LDLGNGCFNL THTCDSNCVN SISRG TYTR ENYIHNVTLA GTPKIDGVV

UniProtKB: Hemagglutinin

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 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: 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: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1164981
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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