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- EMDB-76455: Cryo-EM structure of B/Phuket/3037/2013 hemagglutinin trimer in c... -

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Basic information

Entry
Database: EMDB / ID: EMD-76455
TitleCryo-EM structure of B/Phuket/3037/2013 hemagglutinin trimer in complex with two KL-BHA-3D7 Fab fragments
Map dataCryo-EM structure of B/Phuket/3073/2013 trimer in complex with two KL-BHA-3D7 Fab fragments
Sample
  • Complex: Cryo-EM structure of B/Phuket/3073/2013 hemagglutinin trimer in complex with two KL-BHA-3D7 Fab fragments
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: KL-BHA-3D7 heavy chain
    • Protein or peptide: KL-BHA-3D7 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshemagglutinin / Fab / viral glycoprotein / Viral protein-Immune System complex
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 speciesMus musculus (house mouse) / Influenza B virus (B/Beijing/13-21/2013)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.98 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/Phuket/3037/2013 hemagglutinin trimer in complex with two KL-BHA-3D7 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_76455.png

Downloads & links

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Map

FileDownload / File: emd_76455.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of B/Phuket/3073/2013 trimer in complex with two KL-BHA-3D7 Fab fragments
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 480 pix.
= 406.08 Å		0.85 Å/pix.
x 480 pix.
= 406.08 Å		0.85 Å/pix.
x 480 pix.
= 406.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.846 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.0018246733 - 1.9221586
Average (Standard dev.)0.00061936985 (±0.018684708)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 406.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_76455_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_76455_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/Phuket/3073/2013 hemagglutinin trimer in c...

EntireName: Cryo-EM structure of B/Phuket/3073/2013 hemagglutinin trimer in complex with two KL-BHA-3D7 Fab fragments
Components
  • Complex: Cryo-EM structure of B/Phuket/3073/2013 hemagglutinin trimer in complex with two KL-BHA-3D7 Fab fragments
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: KL-BHA-3D7 heavy chain
    • Protein or peptide: KL-BHA-3D7 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of B/Phuket/3073/2013 hemagglutinin trimer in c...

SupramoleculeName: Cryo-EM structure of B/Phuket/3073/2013 hemagglutinin trimer in complex with two KL-BHA-3D7 Fab fragments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: B/Phuket/3073/2013 hemagglutinin expressed using Sf9 insect cells
Source (natural)Organism: Mus musculus (house mouse)

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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 B virus (B/Beijing/13-21/2013) / Strain: B/Beijing/13-21/2013
Molecular weightTheoretical: 56.616316 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DRICTGITSS NSPHVVKTAT QGEVNVTGVI PLTTTPTKSY FANLKGTRTR GKLCPDCLNC TDLDVALGRP MCVGTTPSAK ASILHEVRP VTSGCFPIMH DRTKIRQLPN LLRGYEKIRL STQNVIDAEK APGGPYRLGT SGSCPNATSK IGFFATMAWA V PKDNYKNA ...String:
DRICTGITSS NSPHVVKTAT QGEVNVTGVI PLTTTPTKSY FANLKGTRTR GKLCPDCLNC TDLDVALGRP MCVGTTPSAK ASILHEVRP VTSGCFPIMH DRTKIRQLPN LLRGYEKIRL STQNVIDAEK APGGPYRLGT SGSCPNATSK IGFFATMAWA V PKDNYKNA TNPLTVEVPY ICTEGEDQIT VWGFHSDNKI QMKSLYGDSN PQKFTSSANG VTTHYVSQIG DFPDQTEDGG LP QSGRIVV DYMMQKPGKT GTIVYQRGVL LPQKVWCASG RSKVIKGSLP LIGEADCLHE EYGGLNKSKP YYTGKHAKAI GNC PIWVKT PLKLANGTKY RPPAKLLKER GFFGAIAGFL EGGWEGMIAG WHGYTSHGAH GVAVAADLKS TQEAINKITK NLNS LSELE VKNLQRLSGA MDELHNEILE LDEKVDDLRA DTISSQIELA VLLSNEGIIN SEDEHLLALE RKLKKMLGPS AVDIG NGCF ETKHKCNQTC LDRIAAGTFN AGEFSLPTFD SLNITAAS

UniProtKB: Hemagglutinin

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Macromolecule #2: KL-BHA-3D7 heavy chain

MacromoleculeName: KL-BHA-3D7 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.419956 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DVQLVESGGG LVQPGGSRKL SCAASGFTFS SFGMHWVRQA PEKGLEWVAY ISSGSTIIYY ADTVKGRFTI SRDNPKNTLF LQMTSLRSE DTAMYYCARS GSSYVRDWYF DVWGAGTTVT VSS

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Macromolecule #3: KL-BHA-3D7 light chain

MacromoleculeName: KL-BHA-3D7 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.192493 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString:
DIVLTQSPAS LAVSLGQRAT ISCRASESVD YYGDSFMHWY QQKPGQPPKL LIYRASNLES GIPARFSGSG SRTDFTLTIN PVEADDVAT YFCQQSNQDP WTFGGGTKLE IK

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / 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: 7.5
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: 58.69 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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 118085
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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