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Yorodumi- EMDB-76453: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex w... -
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Basic information
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| Title | Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments | ||||||||||||||||||
Map data | structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments | ||||||||||||||||||
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Keywords | hemagglutinin / Fab / viral glycoprotein / Viral Protein-Immune System complex | ||||||||||||||||||
| Function / homology | : Function and homology information | ||||||||||||||||||
| Biological species | ![]() Influenza B virus (B/Lee/1940) | ||||||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||||||||||||||
Authors | Civljak A / Bonnettaz B / Bajic G | ||||||||||||||||||
| Funding support | United States, 5 items
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Citation | Journal: J Virol / Year: 2026Title: Broadly reactive antibodies against influenza B virus hemagglutinin neutralize and protect through distinct structural mechanisms. Authors: Disha Bhavsar / Alesandro Civljak / Bruno Bonnettaz / Guha Asthagiri Arunkumar / Florian Krammer / Goran Bajic / ![]() Abstract: Influenza B viruses contribute substantially to seasonal disease burden; however, the structural basis by which antibodies recognize the major glycoprotein hemagglutinin (HA) and mediate antiviral ...Influenza B viruses contribute substantially to seasonal disease burden; however, the structural basis by which antibodies recognize the major glycoprotein hemagglutinin (HA) and mediate antiviral activity remains incompletely defined. Influenza B virus used to circulate as two antigenically distinct lineages, B/Victoria/2/1987-like and B/Yamagata/16/1988-like, although the latter has not been detected in global surveillance in recent years. Antigenic drift in HA contributes to reduced vaccine effectiveness; however, the structural and functional basis by which antibodies recognize influenza B virus HA and mediate antiviral activity remains incompletely defined and thus thwarts our efforts in guiding next-generation vaccine design for broad protection. We characterize four murine monoclonal antibodies (mAb) that broadly bind and neutralize influenza B viruses spanning isolates across four decades of antigenic drift. Using cryo-electron microscopy coupled with and functional assays, we show that these antibodies target distinct regions of HA and confer antiviral activity through multiple mechanisms. One antibody engages the receptor-binding site and potently inhibits hemagglutination, whereas others interfere with viral egress and inhibit neuraminidase (NA) activity, suggesting steric occlusion of NA. A medial-junction antibody additionally induces antibody-dependent cellular cytotoxicity . Despite these mechanistic differences, all antibodies confer complete protection in mice when administered prophylactically or therapeutically. Together, these findings define distinct modes of antibody recognition of influenza B virus HA and link epitope specificity to antiviral function, providing a mechanistic understanding of correlates of immune protection and informing efforts to elicit broadly protective antibody responses against influenza B viruses.IMPORTANCEInfluenza B viruses cause substantial seasonal illness, particularly in children; however, antibody responses against influenza B virus remain less well understood than those against influenza A virus. Here, we identified four antibodies that broadly recognize influenza B virus hemagglutinin and protect through distinct mechanisms. We determined cryo-electron microscopy structures of three antibody-hemagglutinin complexes to define their epitopes and explain their molecular mechanisms of action. One antibody blocks viral attachment by engaging the receptor-binding site, whereas antibodies targeting the medial junction act through post-entry antiviral activity, neuraminidase inhibition, or immune effector functions. Although the antibodies differed in neutralizing potency, all protected mice when administered before infection, and several remained effective after infection. These findings show that broad protection against influenza B virus can arise through multiple antibody targets and mechanisms, informing the evaluation and design of future vaccines and antibody-based therapies. | ||||||||||||||||||
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Structure visualization
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Downloads & links
-EMDB archive
| Map data | emd_76453.map.gz | 368.4 MB | EMDB map data format | |
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| Header (meta data) | emd-76453-v30.xml emd-76453.xml | 22.5 KB 22.5 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_76453_fsc.xml | 15.8 KB | Display | FSC data file |
| Images | emd_76453.png | 118 KB | ||
| Filedesc metadata | emd-76453.cif.gz | 6.7 KB | ||
| Others | emd_76453_half_map_1.map.gz emd_76453_half_map_2.map.gz | 392 MB 392 MB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-76453 ftp://data.pdbj.org/pub/emdb/structures/EMD-76453 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 12idMC ![]() 12ieC ![]() 12ifC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Map
| File | Download / File: emd_76453.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.829 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: Half Map B
| File | emd_76453_half_map_1.map | ||||||||||||
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| Annotation | Half Map B | ||||||||||||
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| Density Histograms |
-Half map: Half Map A
| File | emd_76453_half_map_2.map | ||||||||||||
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| Annotation | Half Map A | ||||||||||||
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Sample components
-Entire : Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex w...
| Entire | Name: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments |
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| Components |
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-Supramolecule #1: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex w...
| Supramolecule | Name: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-3F4 Fab fragments type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: B/Lee/1940 hemagglutinin expressed using Sf9 insect cells |
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| Source (natural) | Organism: ![]() |
-Macromolecule #1: Hemagglutinin
| Macromolecule | Name: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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| Source (natural) | Organism: Influenza B virus (B/Lee/1940) / Strain: B/Lee/1940 |
| Molecular weight | Theoretical: 56.640168 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: DRICTGITSS NSPHVIKTAT QGEVNVTGVI PLTTTPTRSH FANLKGTQTR GKLCPNCFDC TDLDVALGRP KCMGNIPSAK VSILHEVKP VTSGCFPIMH DRTKIRQLPN LLRGYENIRL STSNVINAET APGGPYKVGT SGSCPNVANR NGFFNTMAWV I PQDNNKTA ...String: DRICTGITSS NSPHVIKTAT QGEVNVTGVI PLTTTPTRSH FANLKGTQTR GKLCPNCFDC TDLDVALGRP KCMGNIPSAK VSILHEVKP VTSGCFPIMH DRTKIRQLPN LLRGYENIRL STSNVINAET APGGPYKVGT SGSCPNVANR NGFFNTMAWV I PQDNNKTA INPVTVEVPY ICSEGEDQIT VWGFHSDDKT QMERLYGDSN PQKFTSSANG VTTHYVSQIG GFPNQTEDEG LK QSGRIVV DYMVQKPGKT GTIVYQRGIL LPQKVWCASG RSKVIKGSLP LIGEADCLHE KYGGLNKSKP YYTGEHAKAI GNC PIWVKT PLKLANGTKY RPPAKLLKER GFFGAIAGFL EGGWEGMIAG WHGYTSHGAH GVAVAADLKS TQEAINKITK NLNS LSELE VKNLQRLSGA MNGLHDEILE LDEKVDDLRA DTISSQIELA VLLSNEGIIN SEDEHLLALE RKLKKMLGPS AVEIG NGCF ETKHKCNQTC LDRIAAGTFN AGDFSLPTFD SLNITAAS UniProtKB: UNIPROTKB: Q0PLR5 |
-Macromolecule #2: KL-BHA-3F4 heavy chain
| Macromolecule | Name: KL-BHA-3F4 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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| Source (natural) | Organism: ![]() |
| Molecular weight | Theoretical: 13.816409 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: KVQLQQSGAG LVKPGASVKL SCKASGYTFT EYIIHWVKQR SGQGLEWIGW FYPGSGSIRF NEKFKDKATL TADKSSSTVY MELSRLTSE DSAVYFCARH GSIYYDYQGY FDYWGQGTTL TVSS |
-Macromolecule #3: KL-BHA-3F4 light chain
| Macromolecule | Name: KL-BHA-3F4 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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| Source (natural) | Organism: ![]() |
| Molecular weight | Theoretical: 11.934287 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: DIVMTQSHKF MSTSVGDRVS ITCKASQDVS STIAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTD FTLTISNVRA EDLTLYYCQ QHYSSPWTFG GGTYLEIK |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
| Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 10 / Formula: NAG |
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| Molecular weight | Theoretical: 221.208 Da |
| Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.59 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: SPOT SCAN / 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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About Yorodumi



Keywords
Influenza B virus (B/Lee/1940)
Authors
United States, 5 items
Citation





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Processing
FIELD EMISSION GUN

