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- EMDB-65498: Cryo-EM structure of spiny eel influenza-like virus HA and GM2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-65498
TitleCryo-EM structure of spiny eel influenza-like virus HA and GM2 complex
Map data
Sample
  • Complex: spiny eel influenza-like virus HA and GM2 complex
KeywordsHA / GM2 / PROTEIN BINDING
Biological speciesWuhan spiny eel influenza virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsSun JQ / Gao F
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) 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
DepositionJul 24, 2025-
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_65498.png

Downloads & links

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Map

FileDownload / File: emd_65498.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 300 pix.
= 267. Å		0.89 Å/pix.
x 300 pix.
= 267. Å		0.89 Å/pix.
x 300 pix.
= 267. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.4203747 - 1.1977887
Average (Standard dev.)-0.0016185839 (±0.036445234)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 267.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65498_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_65498_half_map_2.map
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Sample components

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Entire : spiny eel influenza-like virus HA and GM2 complex

EntireName: spiny eel influenza-like virus HA and GM2 complex
Components
  • Complex: spiny eel influenza-like virus HA and GM2 complex

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Supramolecule #1: spiny eel influenza-like virus HA and GM2 complex

SupramoleculeName: spiny eel influenza-like virus HA and GM2 complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Wuhan spiny eel influenza virus

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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: 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 ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 330717
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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