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- EMDB-49475: Computationally optimized broadly reactive influenza B hemaggluti... -

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Basic information

Entry
Database: EMDB / ID: EMD-49475
TitleComputationally optimized broadly reactive influenza B hemagglutinin BC2 bound by antibody #3978
Map datasharpened map after spIsoNet correction
Sample
  • Complex: Complex of a viral protein with an antibody
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Fab A Heavy Chain
    • Protein or peptide: Fab A Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza / antibody / cell entry / hemagglutination / VIRAL PROTEIN / 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 speciesHomo sapiens (human) / Influenza B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.36 Å
AuthorsDzimianski JV / Kunkel I / Balasco Serrao VH / DuBois RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00052 United States
CitationJournal: To Be Published
Title: Computationally optimized broadly reactive influenza B hemagglutinin BC2 bound by antibodies #46 and #3978
Authors: Dzimianski JV / Kunkel I / Balasco Serrao VH / DuBois RM
History
DepositionFeb 26, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49475.png

Downloads & links

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Map

FileDownload / File: emd_49475.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map after spIsoNet correction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.57 Å/pix.
x 576 pix.
= 329.875 Å		0.57 Å/pix.
x 576 pix.
= 329.875 Å		0.57 Å/pix.
x 576 pix.
= 329.875 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.5727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.79456 - 3.015668
Average (Standard dev.)-0.0002298655 (±0.036777884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 329.8752 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49475_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_49475_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: spIsoNet corrected half map B

Fileemd_49475_additional_2.map
AnnotationspIsoNet corrected half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: spIsoNet corrected half map A

Fileemd_49475_additional_3.map
AnnotationspIsoNet corrected half 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_49475_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_49475_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of a viral protein with an antibody

EntireName: Complex of a viral protein with an antibody
Components
  • Complex: Complex of a viral protein with an antibody
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Fab A Heavy Chain
    • Protein or peptide: Fab A Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of a viral protein with an antibody

SupramoleculeName: Complex of a viral protein with an antibody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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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
Molecular weightTheoretical: 57.375242 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DRICTGITSS NSPHVVKTAT QGEVNVTGVI PLTTTPTKSH FANLKGTKTR GKLCPKCLNC TDLDVALGRP KCMGTIPSAK ASILHEVRP VTSGCFPIMH DRTKIRQLPN LLRGYENIRL STHNVINAEK APGGPYRIGT SGSCPNVTNG NGFFATMAWA V PKNDNNKT ...String:
DRICTGITSS NSPHVVKTAT QGEVNVTGVI PLTTTPTKSH FANLKGTKTR GKLCPKCLNC TDLDVALGRP KCMGTIPSAK ASILHEVRP VTSGCFPIMH DRTKIRQLPN LLRGYENIRL STHNVINAEK APGGPYRIGT SGSCPNVTNG NGFFATMAWA V PKNDNNKT ATNPLTVEVP YICTEGEDQI TVWGFHSDNE TQMKKLYGDS KPQKFTSSAN GVTTHYVSQI GGFPNQTEDG GL PQSGRIV VDYMVQKSGK TGTIVYQRGI LLPQKVWCAS GRSKVIKGSL PLIGEADCLH EKYGGLNKSK PYYTGEHAKA IGN CPIWVK TPLKLANGTK YRPPAKLLKE RGFFGAIAGF LEGGWEGMIA GWHGYTSHGA HGVAVAADLK STQEAINKIT KNLN SLSEL EVKNLQRLSG AMDELHNEIL ELDEKVDDLR ADTISSQIEL AVLLSNEGII NSEDEHLLAL ERKLKKMLGP SAVDI GNGC FETKHKCNQT CLDRIAAGTF NAGEFSLPTF DSLNITAASS GRLVPR

UniProtKB: Hemagglutinin

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Macromolecule #2: Fab A Heavy Chain

MacromoleculeName: Fab A Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.610729 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EVQLVESGGH LVQPGGSLRL SCEASGFSFD EYAMHWVREA PGKGLEWVAG ISWNSGAIGY AGSVKGRFTI SKDSAKRVLY LQMNSLRPE DAALYYCAKD MREGCSGTNC YSYYYYFYAM DVWGQGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
EVQLVESGGH LVQPGGSLRL SCEASGFSFD EYAMHWVREA PGKGLEWVAG ISWNSGAIGY AGSVKGRFTI SKDSAKRVLY LQMNSLRPE DAALYYCAKD MREGCSGTNC YSYYYYFYAM DVWGQGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT H

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Macromolecule #3: Fab A Light Chain

MacromoleculeName: Fab A Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.896277 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QSVLTQPPSV SGAPGQGVTI SCTGSSSNLG ADYDVHWYQH LPGKAPKLLI YDNDKRPPGI PDRFSASRSG PSASLAISGL QGEDEADYY CQSYDSHLSG SVFGGGTKLT VVLGQPKAAP SVTLFPPSSE ELQANKATLV CLISDFYPGA VTVAWKADSS P VKAGVETT ...String:
QSVLTQPPSV SGAPGQGVTI SCTGSSSNLG ADYDVHWYQH LPGKAPKLLI YDNDKRPPGI PDRFSASRSG PSASLAISGL QGEDEADYY CQSYDSHLSG SVFGGGTKLT VVLGQPKAAP SVTLFPPSSE ELQANKATLV CLISDFYPGA VTVAWKADSS P VKAGVETT TPSKQSNNKY AASSYLSLTP EQWKSHRSYS CQVTHEGSTV EKTVAPTEC

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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: 3 / 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 / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number grids imaged: 2 / Number real images: 35025 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1165223
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 185640
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.5.3)
Final 3D classificationNumber classes: 4 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

9nj3

chain_id: A, source_name: PDB, initial_model_type: experimental model

9nj3

chain_id: H, source_name: PDB, initial_model_type: experimental model

9nj3

chain_id: L, source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9nj6:
Computationally optimized broadly reactive influenza B hemagglutinin BC2 bound by antibody #3978

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