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- PDB-9ked: Cryo-EM structure of spiny eel influenza-like virus HA -

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Basic information

Entry
Database: PDB / ID: 9ked
TitleCryo-EM structure of spiny eel influenza-like virus HA
ComponentsHemagglutinin
KeywordsVIRAL PROTEIN / Complex
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsSun, J.Q. / Zhang, D.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,6869
Polymers168,3593
Non-polymers1,3276
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Hemagglutinin


Mass: 56119.637 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Wuhan spiny eel influenza virus / Production host: Homo sapiens (human) / References: UniProt: A0A2P1GNV0
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of spiny eel influenza-like virus HA
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Wuhan spiny eel influenza virus
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42963 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311487
ELECTRON MICROSCOPYf_angle_d0.66815564
ELECTRON MICROSCOPYf_dihedral_angle_d4.3451593
ELECTRON MICROSCOPYf_chiral_restr0.0431788
ELECTRON MICROSCOPYf_plane_restr0.0052016

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