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- EMDB-46466: Map of endoH-treated hemagglutinin A/Sing/INFIMH/16 -

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Basic information

Entry
Database: EMDB / ID: EMD-46466
TitleMap of endoH-treated hemagglutinin A/Sing/INFIMH/16
Map datamap of endoH-treated hemagglutinin A/Sing/INFIMH/16
Sample
  • Complex: trimer of influenza hemagglutinin A/Sing/INFIMH/16
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain, Green fluorescent protein fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza / hemagglutinin / evolution / VIRAL PROTEIN
Function / homology
Function and homology information


viral budding from plasma membrane / bioluminescence / generation of precursor metabolites and energy / 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 ...viral budding from plasma membrane / bioluminescence / generation of precursor metabolites and energy / 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 / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
Hemagglutinin / Green fluorescent protein / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus / Aequorea victoria (jellyfish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsTorrents de la Pena A / Ward AB / de Paiva Froes Rocha R
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural and immunological characterization of the H3 influenza hemagglutinin during antigenic drift.
Authors: Rebeca de Paiva Froes Rocha / Ilhan Tomris / Charles A Bowman / Emma Stevens / Jason Kantorow / Corinna M Plitt / Weiwei Peng / Svearike Oeverdieck / Thales Galdino Andrade / James A ...Authors: Rebeca de Paiva Froes Rocha / Ilhan Tomris / Charles A Bowman / Emma Stevens / Jason Kantorow / Corinna M Plitt / Weiwei Peng / Svearike Oeverdieck / Thales Galdino Andrade / James A Ferguson / Diana D Jung / Rafael Elias Marques / Sander Herfst / Joost Snijder / Srirupa Chakraborty / Alba Torrents de la Peña / Zachary T Berndsen / Robert P de Vries / Andrew B Ward /
Abstract: The quest for a universal influenza vaccine holds great promise for mitigating the global burden of influenza-related morbidity and mortality. However, challenges persist in identifying conserved ...The quest for a universal influenza vaccine holds great promise for mitigating the global burden of influenza-related morbidity and mortality. However, challenges persist in identifying conserved epitopes capable of eliciting robust and durable immune responses. In this study, we explore the influence of glycan evolution on H3 hemagglutinin from 1968 to present day and its impacts on protein structure, antigenicity and immunogenicity by using computational, biochemical and biophysical techniques. Structural characterization of HK/68 and Sing/16 by cryo-electron microscopy shows that while HK/68 is resistant to enzymatic deglycosylation, removal of glycans destabilizes the hyperglycosylated head and membrane-proximal region in Sing/16. Furthermore, the appearance of glycans in Sing/16 hemagglutinin head domain shifts the polyclonal immune response upon vaccination to target the esterase and stem. These insights expand our understanding of glycans beyond their role in protein folding and highlight the interplay among glycan integration and immune recognition to design a universal influenza vaccine.
History
DepositionAug 7, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateJan 7, 2026-
Current statusJan 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46466.png

Downloads & links

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Map

FileDownload / File: emd_46466.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of endoH-treated hemagglutinin A/Sing/INFIMH/16
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 360 pix.
= 414. Å		1.15 Å/pix.
x 360 pix.
= 414. Å		1.15 Å/pix.
x 360 pix.
= 414. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.0368645 - 2.582569
Average (Standard dev.)0.00013745249 (±0.046734486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 414.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46466_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of endoH-treated hemagglutinin A/Sing/INFIMH/16

Fileemd_46466_half_map_1.map
Annotationhalf map of endoH-treated hemagglutinin A/Sing/INFIMH/16
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of endoH-treated hemagglutinin A/Sing/INFIMH/16

Fileemd_46466_half_map_2.map
Annotationhalf map of endoH-treated hemagglutinin A/Sing/INFIMH/16
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : trimer of influenza hemagglutinin A/Sing/INFIMH/16

EntireName: trimer of influenza hemagglutinin A/Sing/INFIMH/16
Components
  • Complex: trimer of influenza hemagglutinin A/Sing/INFIMH/16
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain, Green fluorescent protein fusion
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: trimer of influenza hemagglutinin A/Sing/INFIMH/16

SupramoleculeName: trimer of influenza hemagglutinin A/Sing/INFIMH/16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: C3
Source (natural)Organism: Influenza A virus

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Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 37.598809 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAATLCLG HHAVPNGTIV KTITNDRIEV TNATELVQNS SIGEICDSPH QILDGENCTL IDALLGDPQ CDGFQNKKWD LFVERSKAYS NCYPYDVPDY ASLRSLVASS GTLEFKNESF NWTGVTQNGT SSACIRGSSS S FFSRLNWL ...String:
MPMGSLQPLA TLYLLGMLVA SVLAATLCLG HHAVPNGTIV KTITNDRIEV TNATELVQNS SIGEICDSPH QILDGENCTL IDALLGDPQ CDGFQNKKWD LFVERSKAYS NCYPYDVPDY ASLRSLVASS GTLEFKNESF NWTGVTQNGT SSACIRGSSS S FFSRLNWL THLNYTYPAL NVTMPNKEQF DKLYIWGVHH PGTDKDQIFL YAQSSGRITV STKRSQQAVI PNIGSRPRIR DI PSRISIY WTIVKPGDIL LINSTGNLIA PRGYFKIRSG KSSIMRSDAP IGKCKSECIT PNGSIPNDKP FQNVNRITYG ACP RYVKHS TLKLATGMRN VPEK

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2 chain, Green fluorescent protein fusion

MacromoleculeName: Hemagglutinin HA2 chain, Green fluorescent protein fusion
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Aequorea victoria (jellyfish)
Molecular weightTheoretical: 55.162629 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QTRGIFGAIA GFIENGWEGM VDGWYGFRHQ NSEGRGQAAD LKSTQAAIDQ INGKLNRLIG KTNEKFHQIE KEFSEVEGRV QDLEKYVED TKIDLWSYNA ELLVALENQH TIDLTDSEMN KLFEKTKKQL RENAEDMGNG CFKIYHKCDN ACIESIRNET Y DHNVYRDE ...String:
QTRGIFGAIA GFIENGWEGM VDGWYGFRHQ NSEGRGQAAD LKSTQAAIDQ INGKLNRLIG KTNEKFHQIE KEFSEVEGRV QDLEKYVED TKIDLWSYNA ELLVALENQH TIDLTDSEMN KLFEKTKKQL RENAEDMGNG CFKIYHKCDN ACIESIRNET Y DHNVYRDE ALNNRFQIKR MKQIEDKIEE IESKQKKIEN EIARIKKIKL VPRGSVDENL YFQAMSKGEE LFTGVVPILV EL DGDVNGH KFSVRGEGEG DATNGKLTLK FICTTGKLPV PWPTLVTTLT YGVQCFSRYP DHMKRHDFFK SAMPEGYVQE RTI SFKDDG TYKTRAEVKF EGDTLVNRIE LKGIDFKEDG NILGHKLEYN FNSHNVYITA DKQKNGIKAN FKIRHNVEDG SVQL ADHYQ QNTPIGDGPV LLPDNHYLST QSVLSKDPNE KRDHMVLLEF VTAAGITHGM SSAWSHPQFE KGGGSGGGSG GSAWS HPQF EK

UniProtKB: Hemagglutinin, Green fluorescent protein

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 30 / 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

Concentration1 mg/mL
BufferpH: 7.4 / Details: TBS
GridModel: EMS Lacey Carbon / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1313732
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4m4y

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 52046
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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