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- EMDB-62290: Cryo-EM structure of spiny eel influenza-like virus HA -

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Basic information

Entry
Database: EMDB / ID: EMD-62290
TitleCryo-EM structure of spiny eel influenza-like virus HA
Map data
Sample
  • Complex: Cryo-EM structure of spiny eel influenza-like virus HA
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsComplex / 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: 2.95 Å
AuthorsSun JQ / Zhang D
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB29010202 China
CitationJournal: PLoS Pathog / Year: 2025
Title: The hemagglutinin-like proteins of basal vertebrate influenza-like viruses exhibit sialic-acid receptor binding disparity and their structural bases.
Authors: Di Zhang / Kefang Liu / Yufeng Xie / Junqing Sun / Wei Zhang / Haixia Xiao / Yi Shi / William J Liu / George F Gao / Chuxia Deng / Feng Gao /
Abstract: In 2018, two novel influenza-like virus genomes were first identified in basal vertebrates: the Asiatic toads (Bufo gargarizans) and spiny eels (Mastacembelus aculeatus). Their hemagglutinin (HA) ...In 2018, two novel influenza-like virus genomes were first identified in basal vertebrates: the Asiatic toads (Bufo gargarizans) and spiny eels (Mastacembelus aculeatus). Their hemagglutinin (HA) proteins exhibit remarkably low amino acid sequences homology (23.0% and 42.8%, respectively) compared to influenza B virus (IBV), their closest canonical influenza virus relative. This study revealed that the Asiatic toad influenza-like virus HA (tHA) demonstrates dual receptor specificity, bound both α2-3 (avian-type) and α2-6 (human-type) sialic acid (SA) receptors, whereas the spiny eel influenza-like virus HA (eHA) lacks this capability. Biophysical characterization showed reduced thermal stability (lower Tm values) for both tHA and eHA compared to canonical influenza HA. Furthermore, we determined the cryo-EM structures of apo-tHA, tHA in complex with either α2-3 SA receptor or α2-6 SA receptor, as well as apo-eHA and eHA bound to GM2 complex. Our analysis revealed that tHA has a shorter length and looser HA trimer packing compared to canonical HA. These findings collectively indicate that influenza-like viruses in basal vertebrates have evolutionarily acquired dual SA receptor-binding capacity, a trait critical for cross-species transmission in influenza viruses. However, the observed thermolability of these HA proteins suggests that host physiological temperatures may impose a barrier to zoonotic spillover.
History
DepositionNov 4, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62290.png

Downloads & links

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Map

FileDownload / File: emd_62290.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
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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
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.102
Minimum - Maximum-0.2678431 - 0.6898504
Average (Standard dev.)0.0014124606 (±0.024802573)
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_62290_half_map_1.map
Projections & Slices
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Histogram

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Half map: #2

Fileemd_62290_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of spiny eel influenza-like virus HA

EntireName: Cryo-EM structure of spiny eel influenza-like virus HA
Components
  • Complex: Cryo-EM structure of spiny eel influenza-like virus HA
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of spiny eel influenza-like virus HA

SupramoleculeName: Cryo-EM structure of spiny eel influenza-like virus HA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Wuhan spiny eel 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 spiny eel influenza virus
Molecular weightTheoretical: 56.119637 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DKICAGVASG KGTHRVETIT KGEVLVTNAI NMTHTPTSGP FGDLKTGNVR DKLCPTCTGC TDMDVALMTP TCNGVIPEAI AAIQHENRP LQSKCNPILH DLGNTRQLPN LLRKYKKIRK SSGIAFPLAS YADQPVISNP SGNCRDGNGV ESEFGSLLWL T GNTKGAIT ...String:
DKICAGVASG KGTHRVETIT KGEVLVTNAI NMTHTPTSGP FGDLKTGNVR DKLCPTCTGC TDMDVALMTP TCNGVIPEAI AAIQHENRP LQSKCNPILH DLGNTRQLPN LLRKYKKIRK SSGIAFPLAS YADQPVISNP SGNCRDGNGV ESEFGSLLWL T GNTKGAIT GETITITHQC NNDEVMVLVW GAWADLSATM NTIYGVTTPQ TYVSNFPSGR FSMSPFLGNF PALAETEATT AT GRIYLRM EVLESGQRGT IQYQRGFMGP GKFWCLSEPI PVVKGAVKTN GAVSDCLHEV YGGISKPTPF YTGNRGKSVG NCP KWVRKP LLVVNGTKAR DSISTRGLFG AIAGFLEGGW DGMIAGWHGY SSTGDHGTKV AADLVSTQKA MDAITARINN MNKM TERAF SVTDSTMQEI QKEIKDLDKK IDDVRADETA AQIEMIVLLE NENIINAEDE HVHALKQKLT KMLGPSAQDM GDGCF IVDH QCKEDCLREI VSGNYTPSKY GMDEFKSPII TGTV

UniProtKB: Hemagglutinin

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (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: 2.0 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: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 42963
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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