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- EMDB-50546: Cryo-EM structure of Influenza B/Washington/02/2019 virus hemaggl... -

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Basic information

Entry
Database: EMDB / ID: EMD-50546
TitleCryo-EM structure of Influenza B/Washington/02/2019 virus hemagglutinin in complex with single-domain antibody hVHH-69.
Map dataAnisotropic sharpened map of Influenza B/Washington/02/2019 hemagglutinin in complex with hVHH-69, used for model refinement in Phenix.
Sample
  • Complex: Complex between Influenza B/Washington/02/2019 virus hemagglutinin and single-domain antibody hVHH-69
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Single-domain antibody hVHH-69
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshemagglutinin / single-domain antibody / complex / ANTIVIRAL 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 / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsFelix J / Matthys A / Savvides SN / Saelens X
Funding support Belgium, 3 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)1S93223N Belgium
Other privateFlanders Institute for Biotechnology (VIB) grant C0101
Other privateFlanders Institute for Biotechnology (VIB) grant C0301
CitationJournal: Nat Commun / Year: 2025
Title: Single-domain antibodies directed against hemagglutinin and neuraminidase protect against influenza B viruses
Authors: Matthys A / Felix J / Catani JPP / Roose K / Nerinckx W / Van Buyten B / Fijalkowska D / Callewaert N / Savvides SN / Saelens X
History
DepositionJun 5, 2024-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50546.png

Downloads & links

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Map

FileDownload / File: emd_50546.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAnisotropic sharpened map of Influenza B/Washington/02/2019 hemagglutinin in complex with hVHH-69, used for model refinement in Phenix.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.72 Å/pix.
x 360 pix.
= 259.2 Å		0.72 Å/pix.
x 360 pix.
= 259.2 Å		0.72 Å/pix.
x 360 pix.
= 259.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.22885256 - 0.39110792
Average (Standard dev.)0.00018461127 (±0.010661536)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50546_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened, unfiltered full map of Influenza B/Washington/02/2019 hemagglutinin...

Fileemd_50546_additional_1.map
AnnotationUnsharpened, unfiltered full map of Influenza B/Washington/02/2019 hemagglutinin in complex with hVHH-69, used for map and model validation.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpened map of Influenza B/Washington/02/2019 hemagglutinin in...

Fileemd_50546_additional_2.map
AnnotationDeepEMhancer sharpened map of Influenza B/Washington/02/2019 hemagglutinin in complex with hVHH-69, used for model building and map visualization.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of Influenza B/Washington/02/2019 hemagglutinin in...

Fileemd_50546_half_map_1.map
AnnotationHalf map 2 of Influenza B/Washington/02/2019 hemagglutinin in complex with hVHH-69.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of Influenza B/Washington/02/2019 hemagglutinin in...

Fileemd_50546_half_map_2.map
AnnotationHalf map 1 of Influenza B/Washington/02/2019 hemagglutinin in complex with hVHH-69.
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 between Influenza B/Washington/02/2019 virus hemagglutini...

EntireName: Complex between Influenza B/Washington/02/2019 virus hemagglutinin and single-domain antibody hVHH-69
Components
  • Complex: Complex between Influenza B/Washington/02/2019 virus hemagglutinin and single-domain antibody hVHH-69
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Single-domain antibody hVHH-69
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex between Influenza B/Washington/02/2019 virus hemagglutini...

SupramoleculeName: Complex between Influenza B/Washington/02/2019 virus hemagglutinin and single-domain antibody hVHH-69
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Influenza B virus
Molecular weightTheoretical: 270 KDa

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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: 65.530621 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLGDRICTG ITSSNSPHVV KTATQGEVNV TGVIPLTTTP TKSHFANLKG TETRGKLCPK CLNCTDLDV ALGRPKCTGK IPSARVSILH EVRPVTSGCF PIMHDRTKIR QLPNLLRGYE HVRLSTHNVI NAEDAPGRPY E IGTSGSCP ...String:
MPMGSLQPLA TLYLLGMLVA SVLGDRICTG ITSSNSPHVV KTATQGEVNV TGVIPLTTTP TKSHFANLKG TETRGKLCPK CLNCTDLDV ALGRPKCTGK IPSARVSILH EVRPVTSGCF PIMHDRTKIR QLPNLLRGYE HVRLSTHNVI NAEDAPGRPY E IGTSGSCP NITNGNGFFA TMAWAVPKNK TATNPLTIEV PYICTEGEDQ ITVWGFHSDN ETQMAKLYGD SKPQKFTSSA NG VTTHYVS QIGGFPNQTE DGGLPQSGRI VVDYMVQKSG KTGTITYQRG ILLPQKVWCA SGRSKVIKGS LPLIGEADCL HEK YGGLNK SKPYYTGEHA KAIGNCPIWV KTPLKLANGT KYRPPAKLLK ERGFFGAIAG FLEGGWEGMI AGWHGYTSHG AHGV AVAAD LKSTQEAINK ITKNLNSLSE LEVKNLQRLS GAMDELHNEI LELDEKVDDL RADTISSQIE LAVLLSNEGI INSED EHLL ALERKLKKML GPSAVEIGNG CFETKHKCNQ TCLDRIAAGT FDAGEFSLPT FDSLNITAAS LNDDGLDNHT ISGKRM KQI EDKIEEIESK QKKIENEIAR IKKLIGERSA WSHPQFEK

UniProtKB: Hemagglutinin

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Macromolecule #2: Single-domain antibody hVHH-69

MacromoleculeName: Single-domain antibody hVHH-69 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.521857 KDa
Recombinant expressionOrganism: Komagataella phaffii (fungus)
SequenceString:
DVQLVESGGG LVQPGGSLRL SCAASGLVDS ANVAWFRQAP GKEREFVAAV KWRSGSTIYA DSVEGRFTIS RDNAKSTVYL QMNSLRPED TAVYYCAANQ WYSGGYYGEK NYDYWGQGTL VTVSS

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / 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

Concentration0.4 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
0.137 MSodium chloride
0.0027 MPotassium Chloride
0.01 MSodium Phosphate Dibasic
0.0018 MPotassium Phosphate Monobasic
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4352 / Average electron dose: 60.0 e/Å2
Details: Images were collected at 40 degree tilt to overcome preferred orientations.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

Particle selectionNumber selected: 4124258
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2) / 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: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 157829
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 4.2)
FSC plot (resolution estimation)

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