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- EMDB-60516: Structure of hemagglutinin from HN/4-10 H3N8 influenza virus G228... -

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Basic information

Entry
Database: EMDB / ID: EMD-60516
TitleStructure of hemagglutinin from HN/4-10 H3N8 influenza virus G228 mutant complexed with avian receptor analog LSTa
Map data
Sample
  • Complex: HN/4-10 H3N8 G228 HA complexed with LSTa
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsH3N8 / hemagglutinin / avian receptor / VIRAL PROTEIN
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.09 Å
AuthorsHao TJ / Xie YF / Chai Y / Song H / Gao GF
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
DepositionJun 12, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60516.png

Downloads & links

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Map

FileDownload / File: emd_60516.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.225
Minimum - Maximum-0.42221355 - 1.2670887
Average (Standard dev.)-0.00021301152 (±0.03683023)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60516_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_60516_half_map_2.map
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Sample components

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Entire : HN/4-10 H3N8 G228 HA complexed with LSTa

EntireName: HN/4-10 H3N8 G228 HA complexed with LSTa
Components
  • Complex: HN/4-10 H3N8 G228 HA complexed with LSTa
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HN/4-10 H3N8 G228 HA complexed with LSTa

SupramoleculeName: HN/4-10 H3N8 G228 HA complexed with LSTa / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Influenza A virus

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Details: HN/4-10 H3N8 G228 HA complexed with LSTa / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 57.124691 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: LQQNLPGKDS STATLCLGHH SVPNGTIVKT ITDDQIEVTN ATELVQNSST GKICNNPHKV LDGRDCTLID AMLGDPHCDV FQDEKWDLF VERSSAFSNC YPYDVPDYAS LRSLIASSGT LDFITESFTW AGVSQNGGSS ACKRGPANGF FSRLNWLTKS G SSYPLLNV ...String:
LQQNLPGKDS STATLCLGHH SVPNGTIVKT ITDDQIEVTN ATELVQNSST GKICNNPHKV LDGRDCTLID AMLGDPHCDV FQDEKWDLF VERSSAFSNC YPYDVPDYAS LRSLIASSGT LDFITESFTW AGVSQNGGSS ACKRGPANGF FSRLNWLTKS G SSYPLLNV TMPNNYNFDK LYIWGVHHPS TNQEQTNLYV QASGRVTVST RRSQQTIVPN IGSRPWVRGQ SGRISIYWTI VK PGDVLVI NSNGNLIAPR GFFKIRTGRS SIMRSDAPIE TCISECITPN GSIPNDKPFQ NVNKITYGAC PKYVKQNTLK LAT GMRNVP EKQTRGLFGA IAGFIENGWE GMIDGWYGFR HQNSEGTGQA ADLKSTQAAI DQINGKLNRV IEKTNEKFHQ IEKE FSEVE GRIQDLEKYV EDTKVDLWSY NAELLVALEN QHTIDLTDSE MNKLFEKTRR QLRENAEDMG NGCFKIYHKC DNACI ESIR NGTYDHDIYR DEALNNRFQI RGVEF

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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: 3 / 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: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 2.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 279549
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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