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- EMDB-42060: Cryo-EM structure of prefusion-stabilized influenza B hemagglutinin -

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Basic information

Entry
Database: EMDB / ID: EMD-42060
TitleCryo-EM structure of prefusion-stabilized influenza B hemagglutinin
Map data
Sample
  • Complex: prefusion-stabilized influenza B hemagglutinin
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsCryo-EM / FluB / HA / VIRAL PROTEIN
Function / homology
Function and homology information


viral budding from plasma membrane / 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 / virion 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 speciesInfluenza B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsJuraszek J / Milder FJ / Yu X / Blokland S / Overveld D / Tamara S / Bakkers MJG / Rutten L / Sharma S / Langedijk JPM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: PNAS Nexus / Year: 2024
Title: Engineering a cleaved, prefusion-stabilized influenza B virus hemagglutinin by identification and locking of all six pH switches.
Authors: Jarek Juraszek / Fin J Milder / Xiaodi Yu / Sven Blokland / Daan van Overveld / Pravien Abeywickrema / Sem Tamara / Sujata Sharma / Lucy Rutten / Mark J G Bakkers / Johannes P M Langedijk /
Abstract: Vaccine components based on viral fusion proteins require high stability of the native prefusion conformation for optimal potency and manufacturability. In the case of influenza B virus hemagglutinin ...Vaccine components based on viral fusion proteins require high stability of the native prefusion conformation for optimal potency and manufacturability. In the case of influenza B virus hemagglutinin (HA), the stem's conformation relies on efficient cleavage. In this study, we identified six pH-sensitive regions distributed across the entire ectodomain where protonated histidines assume either a repulsive or an attractive role. Substitutions in these areas enhanced the protein's expression, quality, and stability in its prefusion trimeric state. Importantly, this stabilization enabled the production of a cleavable HA0, which is further processed into HA1 and HA2 by furin during exocytic pathway passage, thereby facilitating correct folding, increased stability, and screening for additional stabilizing substitutions in the core of the metastable fusion domain. Cryo-EM analysis at neutral and low pH revealed a previously unnoticed pH switch involving the C-terminal residues of the natively cleaved HA1. This switch keeps the fusion peptide in a clamped state at neutral pH, averting premature conformational shift. Our findings shed light on new strategies for possible improvements of recombinant or genetic-based influenza B vaccines.
History
DepositionSep 20, 2023-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42060.png

Downloads & links

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Map

FileDownload / File: emd_42060.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 280 pix.
= 254.8 Å		0.91 Å/pix.
x 280 pix.
= 254.8 Å		0.91 Å/pix.
x 280 pix.
= 254.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-2.3965614 - 3.0742452
Average (Standard dev.)0.00028459626 (±0.07699726)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 254.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42060_msk_1.map
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Additional map: #1

Fileemd_42060_additional_1.map
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Half map: #1

Fileemd_42060_half_map_1.map
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Half map: #2

Fileemd_42060_half_map_2.map
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Sample components

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Entire : prefusion-stabilized influenza B hemagglutinin

EntireName: prefusion-stabilized influenza B hemagglutinin
Components
  • Complex: prefusion-stabilized influenza B hemagglutinin
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: prefusion-stabilized influenza B hemagglutinin

SupramoleculeName: prefusion-stabilized influenza B hemagglutinin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Influenza B 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 B virus
Molecular weightTheoretical: 38.928676 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKAIIVLLMV VTSNADRICT GITSSNSPHV VKTATQGEVN VTGVIPLTTT PTKSHFANLK GTETRGKLCP KCLNCTDLDV ALGRPKCTG KIPSARVSIL HEVRPVTSGC FPIMHDRTKI RQLPNLLRGY EHVRLSTHNV INAEGAPGGP YKIGTSGSCP N ITNGNGFF ...String:
MKAIIVLLMV VTSNADRICT GITSSNSPHV VKTATQGEVN VTGVIPLTTT PTKSHFANLK GTETRGKLCP KCLNCTDLDV ALGRPKCTG KIPSARVSIL HEVRPVTSGC FPIMHDRTKI RQLPNLLRGY EHVRLSTHNV INAEGAPGGP YKIGTSGSCP N ITNGNGFF ATMAWAVPDK NKTATNPLTI EVPYVCTEGE DQITVWGFHS DNETQMAKLY GDSKPQTFTS SANGVTTHYV SQ IGGFPNQ TEDGGLPQSG RIVVDYMVQK SGKTGTITYQ RGILLPQKVW CASGRSKVIK GSLPLIGEAD CLHEKYGGLN KSK PYYTGE HAKAIGNCPI WVKTPLKLAN GTKYRPPAKL LKER

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza B virus
Molecular weightTheoretical: 19.675131 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GFFGAIAGFL EGGWEGMIAG WFGYTSHGAH GVAVAADLKA TQEAINKITK NLNSLSELEV KNLYRLSYAM DELHNEILEL DEKVDDLRA DTISSQIELA VLLSNEGIIN REDWFLLALE RKLKKMLGPS AVEIGNGCFE TKHKCNQTCL DKIAAGTFDA G EFSLPTFD SLNITAGGSE PEA

UniProtKB: Hemagglutinin

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 6 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 481814
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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