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- EMDB-70149: CryoEM structure of Wuhan spiny eel influenza virus (WSEIV) HA -

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Basic information

Entry
Database: EMDB / ID: EMD-70149
TitleCryoEM structure of Wuhan spiny eel influenza virus (WSEIV) HA
Map data
Sample
  • Complex: Wuhan spiny eel influenza virus (WSEIV) HA trimer
    • Protein or peptide: Hemagglutinin HA2 chain
  • Protein or peptide: Hemagglutinin HA1 chain
KeywordsWuhan spiny eel influenza virus / WSEIV / Flu Hemagglutinin / HA / VIRUS / VIRAL PROTEIN
Function / homology
Function and homology information


host cell surface receptor binding / endocytosis involved in viral entry into host cell / 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 / membrane
Similarity search - Function
Haemagglutinin, influenzavirus B / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesWuhan spiny eel influenza virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsHuang J / Han J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: bioRxiv / Year: 2025
Title: Characterization of the glycoproteins of novel fish influenza B-like viruses.
Authors: Gagandeep Singh / Jiachen Huang / Disha Bhavsar / Kirill Vasilev / James A Ferguson / Geert-Jan Boons / Viviana Simon / Robert P de Vries / Julianna Han / Andrew Ward / Florian Krammer /
Abstract: Novel influenza-like virus sequences previously identified in fish and amphibians were found to cluster as a sister clade of influenza B viruses, but have thus far remained uncharacterized. We ...Novel influenza-like virus sequences previously identified in fish and amphibians were found to cluster as a sister clade of influenza B viruses, but have thus far remained uncharacterized. We demonstrate that salamander influenza-like virus (SILV) HA is functionally divergent from influenza B virus HA and does not bind to α 2,3- and α2,6-linked sialic acids. However, the HAs of Siamese algae-eater influenza-like virus (SAEILV) and chum salmon influenza-like virus (CSILV) bind to α2,3 linked sialic acid. Furthermore, SAEILV HA binds to sialyated Lewis X, is activated by human airway enzymes and is fusogenic at a wide range of pH conditions. SAEILV NA has a highly conserved active site and a similar structure to other known NAs. We also determined the cryo-electron microscopy structure of the HA of a previously described virus from the same sister clade, the Wuhan spiny eel influenza virus (WSEIV). Importantly, no cross-reactive antibodies against these HAs or NAs were found in the human serum, suggesting that humans are immunologically naïve to these viruses.
History
DepositionApr 10, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70149.png

Downloads & links

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Map

FileDownload / File: emd_70149.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 288 pix.
= 300.96 Å		1.05 Å/pix.
x 288 pix.
= 300.96 Å		1.05 Å/pix.
x 288 pix.
= 300.96 Å

Surface

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.045 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.6930678 - 2.657415
Average (Standard dev.)0.0011286964 (±0.059004307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 300.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70149_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_70149_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_70149_half_map_2.map
Projections & Slices
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Sample components

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Entire : Wuhan spiny eel influenza virus (WSEIV) HA trimer

EntireName: Wuhan spiny eel influenza virus (WSEIV) HA trimer
Components
  • Complex: Wuhan spiny eel influenza virus (WSEIV) HA trimer
    • Protein or peptide: Hemagglutinin HA2 chain
  • Protein or peptide: Hemagglutinin HA1 chain

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Supramolecule #1: Wuhan spiny eel influenza virus (WSEIV) HA trimer

SupramoleculeName: Wuhan spiny eel influenza virus (WSEIV) HA trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2
Source (natural)Organism: Wuhan spiny eel influenza virus

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Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Wuhan spiny eel influenza virus
Molecular weightTheoretical: 36.282379 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NDKICAGVAS GKGTHRVETI TKGEVLVTNA INMTHTPTSG PFGDLKTGNV RDKLCPTCTG CTDMDVALMT PTCNGVIPEA IAAIQHENR PLQSKCNPIL HDLGNTRQLP NLLRKYKKIR KSSGIAFPLA SYADQPVISN PSGNCRDGNG VESEFGSLLW L TGNTKGAI ...String:
NDKICAGVAS GKGTHRVETI TKGEVLVTNA INMTHTPTSG PFGDLKTGNV RDKLCPTCTG CTDMDVALMT PTCNGVIPEA IAAIQHENR PLQSKCNPIL HDLGNTRQLP NLLRKYKKIR KSSGIAFPLA SYADQPVISN PSGNCRDGNG VESEFGSLLW L TGNTKGAI TGETITITHQ CNNDEVMVLV WGAWADLSAT MNTIYGVTTP QTYVSNFPSG RFSMSPFLGN FPALAETEAT TA TGRIYLR MEVLESGQRG TIQYQRGFMG PGKFWCLSEP IPVVKGAVKT NGAVSDCLHE VYGGISKPTP FYTGNRGKSV GNC PKWVRK PLLVVNGTKA R

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Wuhan spiny eel influenza virus
Molecular weightTheoretical: 19.870354 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
DSISTRGLFG AIAGFLEGGW DGMIAGWHGY SSTGDHGTKV AADLVSTQKA MDAITARINN MNKMTERAFS VTDSTMQEIQ KEIKDLDKK IDDVRADETA AQIEMIVLLE NENIINAEDE HVHALKQKLT KMLGPSAQDM GDGCFIVDHQ CKEDCLREIV S GNYTPSKY GMDEFKSPII TGT

UniProtKB: Hemagglutinin

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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

Concentration0.7 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTrisTris
100.0 mMNaClSodium chloride
0.1 %Octyl-beta-GlucosideOctyl-beta-Glucoside
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS 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: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / Details: CryoSPARC Ab-initio
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 198768
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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