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- EMDB-76454: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-76454
TitleCryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments
Map datastructure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments
Sample
  • Complex: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments
    • Protein or peptide: KL-BHA-4C2 heavy chain
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: KL-BHA-4C2 light chain
Keywordshemagglutinin / Fab / viral glycoprotein / Immune System-Viral Protein complex
Function / homology:
Function and homology information
Biological speciesMus musculus (house mouse) / Influenza B virus (B/Lee/1940)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsCivljak A / Bonnettaz B / Bajic G
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI117287 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI109946 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI097092 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400008C United States
Other private United States
CitationJournal: To Be Published
Title: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments
Authors: Civljak A / Bonnettaz B / Bajic G
History
DepositionApr 7, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76454.png

Downloads & links

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Map

FileDownload / File: emd_76454.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 512 pix.
= 432.128 Å		0.84 Å/pix.
x 512 pix.
= 432.128 Å		0.84 Å/pix.
x 512 pix.
= 432.128 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.844 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.001797935 - 2.133005
Average (Standard dev.)0.00047048042 (±0.016254606)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 432.128 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_76454_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_76454_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex w...

EntireName: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments
Components
  • Complex: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments
    • Protein or peptide: KL-BHA-4C2 heavy chain
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: KL-BHA-4C2 light chain

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Supramolecule #1: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex w...

SupramoleculeName: Cryo-EM structure of B/Lee/1940 hemagglutinin trimer in complex with three KL-BHA-4C2 Fab fragments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: B/Lee/1940 hemagglutinin expressed using Sf9 insect cells
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: KL-BHA-4C2 heavy chain

MacromoleculeName: KL-BHA-4C2 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.255941 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
QVTLKESGPG ILRPSQTLSL TCSFSGFSLS TSGMGVGWIR QPSGKGLEWL AHVWWDDDKY YNPSLKSGLT ISKDTSRNQV FLKITSVDT ADSATYYCAR KVLFMRAMDY WGQGTSVTVS S

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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 B virus (B/Lee/1940) / Strain: B/Lee/1940
Molecular weightTheoretical: 56.640168 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #3: KL-BHA-4C2 light chain

MacromoleculeName: KL-BHA-4C2 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.289717 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DIVLIRLTIG QAVVSTQRAT ISCRASESVD SYGNIYMHWY QQKPGQPPKL LIYRASNLES GIPARFSGSG SRTDFTLTIN PVEADDVAT YYCQQSTEDP WTFGGGTKLE IK

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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: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.92 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 80242
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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