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- EMDB-60014: The cryoEM structure of H5N8 HA in an auto inhibited state -

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Basic information

Entry
Database: EMDB / ID: EMD-60014
TitleThe cryoEM structure of H5N8 HA in an auto inhibited state
Map data
Sample
  • Complex: H5N8 HA ectodomain
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsInfluenza / glycosylation / sialic acid / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLi R / Gao J / Wang L / Gui M / Xiang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Npj Viruses / Year: 2024
Title: Multivalent interactions between fully glycosylated influenza virus hemagglutinins mediated by glycans at distinct N-glycosylation sites.
Authors: Ruofan Li / Jingjing Gao / Lin Wang / Miao Gui / Ye Xiang /
Abstract: The hemagglutinin (HA) glycoprotein of influenza virus binds host cell receptors and mediates viral entry. Here we present cryo-EM structures of fully glycosylated HAs from H5N1 and H5N8 influenza ...The hemagglutinin (HA) glycoprotein of influenza virus binds host cell receptors and mediates viral entry. Here we present cryo-EM structures of fully glycosylated HAs from H5N1 and H5N8 influenza viruses. We find that the H5N1 HA can form filaments that comprise two head-to-head HA trimers. Multivalent interactions between the two HA trimers are mediated by glycans attached to N158. The distal Sia1-Gal2-NAG3 sugar moiety of N158 interacts with the receptor binding site on the opposing HA trimer. Additional interactions are observed between NAG3 and residues K222 and K193. The H5N8 HA lacks the N158 glycosylation site and does not form the filamentous structure. However, the H5N8 HA exhibits an auto-inhibition conformation, where the receptor binding site is occupied by the glycan chain attached to residue N169 from a neighboring protomer. These structures represent native HA-glycan interactions, which may closely mimic the receptor-HA interactions on the cell surface.
History
DepositionMay 3, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60014.png

Downloads & links

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Map

FileDownload / File: emd_60014.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.995 Å		1.07 Å/pix.
x 256 pix.
= 274.995 Å		1.07 Å/pix.
x 256 pix.
= 274.995 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.855
Minimum - Maximum-4.243911 - 6.0000377
Average (Standard dev.)0.0011672433 (±0.120753035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.9952 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60014_half_map_1.map
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Half map: #2

Fileemd_60014_half_map_2.map
Projections & Slices
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Sample components

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Entire : H5N8 HA ectodomain

EntireName: H5N8 HA ectodomain
Components
  • Complex: H5N8 HA ectodomain
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: H5N8 HA ectodomain

SupramoleculeName: H5N8 HA ectodomain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Influenza A virus / Strain: A/chicken/Czech_Republic/1566-1/2021
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1
Details: The depositor states that 'For the sequence issues, we only have the GISAID ID: EPI_ISL_977513, since it is not uploaded to uniprot database.'
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 37.793035 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENIVLLLAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCDL NGVKPLILKD CSVAGWLLGN PMCDEFIRV PEWSYIVERA NPSNDLCYPG SLNDYEELKH LLSRINHFEK ILIIPKSSWP NHETSLGVSA ACPYQGAPSF F RNVVWLIK ...String:
MENIVLLLAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCDL NGVKPLILKD CSVAGWLLGN PMCDEFIRV PEWSYIVERA NPSNDLCYPG SLNDYEELKH LLSRINHFEK ILIIPKSSWP NHETSLGVSA ACPYQGAPSF F RNVVWLIK KNDAYPTIKI SYNNTNQEDL LILWGIHHSN NAEEQTNLYK NPTTYISVGT STLNQRLVPK IATRSQVNGQ RG RMDFFWT ILKPDDAIHF ESNGNFIAPE YAYKIVKKGD STIMKSGVEY GHCNTKCQTP VGAINSSMPF HNIHPLTIGE CPK YVKSNK LVLATGLRNS

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 21.995514 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
PLREKRRKRG LFGAIAGFIE GGWQGMVDGW YGYHHSNEQG SGYAADKEST QKAIDGVTNK VNSIIDKMNT QFEAVGREFN NLERRIENL NKKMEDGFLD VWTYNAELLV LMENERTLDF HDSNVKNLYD KVRLQLRDNA KELGNGCFEF YHKCDNECME S VRNGTYDY PQYSGEARLK REEISGVKLE SI

UniProtKB: Hemagglutinin

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 12 / 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: 2.5 µm / Nominal defocus min: 1.5 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: PDB ENTRY
PDB model - PDB ID:

2fk0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 299040
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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