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- EMDB-60015: The cryoEM structure of H5N1 HA split from symmetric filament in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-60015
TitleThe cryoEM structure of H5N1 HA split from symmetric filament in conformation A
Map data
Sample
  • Complex: split trimer of H5N1 HA-FabH5M9 complex from symmetric filament
    • Complex: FabH5M9
      • Protein or peptide: H5M9 Fab, light chain
      • Protein or peptide: Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain
    • Complex: H5N1 HA
      • Protein or peptide: Hemagglutinin
      • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsInfluenza / glycosylation / sialic acid / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / identical protein binding / membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain ...Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Hemagglutinin / Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain
Similarity search - Component
Biological speciesInfluenza A virus (strain A/Vietnam/1203/2004 H5N1) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.45 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-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60015.png

Downloads & links

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Map

FileDownload / File: emd_60015.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 240 pix.
= 316.8 Å		1.32 Å/pix.
x 240 pix.
= 316.8 Å		1.32 Å/pix.
x 240 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.666
Minimum - Maximum-5.395345 - 7.9910555
Average (Standard dev.)0.009243275 (±0.16887547)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60015_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60015_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : split trimer of H5N1 HA-FabH5M9 complex from symmetric filament

EntireName: split trimer of H5N1 HA-FabH5M9 complex from symmetric filament
Components
  • Complex: split trimer of H5N1 HA-FabH5M9 complex from symmetric filament
    • Complex: FabH5M9
      • Protein or peptide: H5M9 Fab, light chain
      • Protein or peptide: Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain
    • Complex: H5N1 HA
      • Protein or peptide: Hemagglutinin
      • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: split trimer of H5N1 HA-FabH5M9 complex from symmetric filament

SupramoleculeName: split trimer of H5N1 HA-FabH5M9 complex from symmetric filament
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus (strain A/Vietnam/1203/2004 H5N1)
Molecular weightTheoretical: 200 KDa

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Supramolecule #2: FabH5M9

SupramoleculeName: FabH5M9 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #3: H5N1 HA

SupramoleculeName: H5N1 HA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (strain A/Vietnam/1203/2004 H5N1)
Molecular weightTheoretical: 38.080363 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEKIVLLFAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KKHNGKLCDL DGVKPLILRD CSVAGWLLGN PMCDEFINV PEWSYIVEKA NPVNDLCYPG DFNDYEELKH LLSRINHFEK IQIIPKSSWS SHEASLGVSS ACPYQGKSSF F RNVVWLIK ...String:
MEKIVLLFAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KKHNGKLCDL DGVKPLILRD CSVAGWLLGN PMCDEFINV PEWSYIVEKA NPVNDLCYPG DFNDYEELKH LLSRINHFEK IQIIPKSSWS SHEASLGVSS ACPYQGKSSF F RNVVWLIK KNSTYPTIKR SYNNTNQEDL LVLWGIHHPN DAAEQTKLYQ NPTTYISVGT STLNQRLVPR IATRSKVNGQ SG RMEFFWT ILKPNDAINF ESNGNFIAPE YAYKIVKKGD STIMKSELEY GNCNTKCQTP MGAINSSMPF HNIHPLTIGE CPK YVKSNR LVLATGLRNS P

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 (strain A/Vietnam/1203/2004 H5N1)
Molecular weightTheoretical: 26.147387 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QRERRRKKRG LFGAIAGFIE GGWQGMVDGW YGYHHSNEQG SGYAADKEST QKAIDGVTNK VNSIIDKMNT QFEAVGREFN NLERRIENL NKKMEDGFLD VWTYNAELLV LMENERTLDF HDSNVKNLYD KVRLQLRDNA KELGNGCFEF YHKCDNECME S VRNGTYDY ...String:
QRERRRKKRG LFGAIAGFIE GGWQGMVDGW YGYHHSNEQG SGYAADKEST QKAIDGVTNK VNSIIDKMNT QFEAVGREFN NLERRIENL NKKMEDGFLD VWTYNAELLV LMENERTLDF HDSNVKNLYD KVRLQLRDNA KELGNGCFEF YHKCDNECME S VRNGTYDY PQYSEEARLK REEISGVKLE SIGIYQILSI YSTVASSLAL AIMVAGLSLW MCSNGSLQCR

UniProtKB: Hemagglutinin

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Macromolecule #3: H5M9 Fab, light chain

MacromoleculeName: H5M9 Fab, light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.946344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVLTQSPGS LTVSLGQRAT ISCRASESVD NFGKSFMHWY QQKPGQSPKL LIYRASNREF GIPARFNGSG SGTDFALTIN PVEADDVAT YFCQQSNEDP RTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT ...String:
DIVLTQSPGS LTVSLGQRAT ISCRASESVD NFGKSFMHWY QQKPGQSPKL LIYRASNREF GIPARFNGSG SGTDFALTIN PVEADDVAT YFCQQSNEDP RTFGGGTKLE IKRADAAPTV SIFPPSSEQL TSGGASVVCF LNNFYPKDIN VKWKIDGSER Q NGVLNSWT DQDSKDSTYS MSSTLTLTKD EYERHNSYTC EATHKTSTSP IVKSFNRNE

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Macromolecule #4: Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain

MacromoleculeName: Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain
type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.935797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVHLQQSGPE LVKPGASVKM SCKTSGYTFT EYTIHWMKQS HGKSLEWIGG IFPNNGDTTY NQKFKVRATL TVGRSSSTAY MDLRSLTSE DSAVYYCVRN YGSSYGYFDV WGAGTTVTVS SAKTTPPSVY PLAPGSAAQT NSMVTLGCLV KGYFPEPVTV T WNSGSLSS ...String:
EVHLQQSGPE LVKPGASVKM SCKTSGYTFT EYTIHWMKQS HGKSLEWIGG IFPNNGDTTY NQKFKVRATL TVGRSSSTAY MDLRSLTSE DSAVYYCVRN YGSSYGYFDV WGAGTTVTVS SAKTTPPSVY PLAPGSAAQT NSMVTLGCLV KGYFPEPVTV T WNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVPSSTWPSE TVTCNVAHPA SSTKVDKKIV PRDC

UniProtKB: Anti-H5N1 hemagglutinin monoclonal anitbody H5M9 heavy chain

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / 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 K2 SUMMIT (4k 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: 3.0 µm / Nominal defocus min: 2.0 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: PDB ENTRY
PDB model - PDB ID:

4mhh

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 216514
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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