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- EMDB-38350: Dual receptor-binding, infectivity, and transmissibility of an em... -

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Basic information

Entry
Database: EMDB / ID: EMD-38350
TitleDual receptor-binding, infectivity, and transmissibility of an emerging H2N2 avian influenza virus
Map data
Sample
  • Complex: The structure of influenza H2 human Singapore hemagglutinin with human receptor
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsH2N2 / influenza virus / receptor / replication / transmission / mice / guinea pig / ferret / mutation / public health risk / VIRUS / VIRAL PROTEIN
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 speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsSun J / Zheng TY
Funding support China, 2 items
OrganizationGrant numberCountry
Chinese Academy of Sciences151C53KYSB20210023 China
Chinese Academy of SciencesYSBR-086 China
CitationJournal: Nat Commun / Year: 2024
Title: Dual receptor-binding, infectivity, and transmissibility of an emerging H2N2 low pathogenicity avian influenza virus.
Authors: Ju Sun / Tianyi Zheng / Mingjun Jia / Yanjun Wang / Jingru Yang / Yun Liu / Pengyun Yang / Yufeng Xie / Honglei Sun / Qi Tong / Jiaming Li / Jing Yang / Guanghua Fu / Yi Shi / Jianxun Qi / ...Authors: Ju Sun / Tianyi Zheng / Mingjun Jia / Yanjun Wang / Jingru Yang / Yun Liu / Pengyun Yang / Yufeng Xie / Honglei Sun / Qi Tong / Jiaming Li / Jing Yang / Guanghua Fu / Yi Shi / Jianxun Qi / Wenjun Liu / Jinhua Liu / Wen-Xia Tian / George F Gao / Yuhai Bi /
Abstract: The 1957 H2N2 influenza pandemic virus [A(H2N2)pdm1957] has disappeared from humans since 1968, while H2N2 avian influenza viruses (AIVs) are still circulating in birds. It is necessary to reveal the ...The 1957 H2N2 influenza pandemic virus [A(H2N2)pdm1957] has disappeared from humans since 1968, while H2N2 avian influenza viruses (AIVs) are still circulating in birds. It is necessary to reveal the recurrence risk and potential cross-species infection of these AIVs from avian to mammals. We find that H2 AIVs circulating in domestic poultry in China have genetic and antigenic differences compared to the A(H2N2)pdm1957. One H2N2 AIV has a dual receptor-binding property similar to that of the A(H2N2)pdm1957. Molecular and structural studies reveal that the N144S, and N144E or R137M substitutions in hemagglutinin (HA) enable H2N2 avian or human viruses to bind or preferentially bind human-type receptor. The H2N2 AIV rapidly adapts to mice (female) and acquires mammalian-adapted mutations that facilitated transmission in guinea pigs and ferrets (female). These findings on the receptor-binding, infectivity, transmission, and mammalian-adaptation characteristics of H2N2 AIVs provide a reference for early-warning and prevention for this subtype.
History
DepositionDec 17, 2023-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38350.png

Downloads & links

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Map

FileDownload / File: emd_38350.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0515
Minimum - Maximum-0.0017187593 - 1.5882232
Average (Standard dev.)0.0012859735 (±0.025682509)
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_38350_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38350_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The structure of influenza H2 human Singapore hemagglutinin with ...

EntireName: The structure of influenza H2 human Singapore hemagglutinin with human receptor
Components
  • Complex: The structure of influenza H2 human Singapore hemagglutinin with human receptor
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: The structure of influenza H2 human Singapore hemagglutinin with ...

SupramoleculeName: The structure of influenza H2 human Singapore hemagglutinin with human receptor
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 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Singapore/1/1957
Molecular weightTheoretical: 56.201922 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DQICIGYHAN NSTETVDTIL ERNVTVTHAK DILEKTHNGK LCKLNGIPPL ELGDCSIAGW LLGNPECDRL LSVPEWSYIM EKENPRDGL CYPGSFNDYE ELKHLLSSVK HFEKVKILPK DRWTQHTTTG GSRACAVSGN PSFFRNMVWL TKKGSNYPVA K GSYNNTSG ...String:
DQICIGYHAN NSTETVDTIL ERNVTVTHAK DILEKTHNGK LCKLNGIPPL ELGDCSIAGW LLGNPECDRL LSVPEWSYIM EKENPRDGL CYPGSFNDYE ELKHLLSSVK HFEKVKILPK DRWTQHTTTG GSRACAVSGN PSFFRNMVWL TKKGSNYPVA K GSYNNTSG EQMLIIWGVH HPNDETEQRT LYQNVGTYVS VGTSTLNKRS TPDIATRPKV NGLGSRMEFS WTLLDMWDTI NF ESTGNLI APEYGFKISK RGSSGIMKTE GTLENCETKC QTPLGAINTT LPFHNVHPLT IGECPKYVKS EKLVLATGLR NVP QIESRG LFGAIAGFIE GGWQGMVDGW YGYHHSNDQG SGYAADKEST QKAFDGITNK VNSVIEKMNT QFEAVGKEFS NLER RLENL NKKMEDGFLD VWTYNAELLV LMENERTLDF HDSNVKNLYD KVRMQLRDNV KELGNGCFEF YHKCDDECMN SVKNG TYDY PKYEEESKLN RNE

UniProtKB: Hemagglutinin

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 8 / 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: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 331328
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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