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- PDB-9fm1: Cryo-EM structure of Influenza B/Washington/02/2019 virus hemaggl... -

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Basic information

Entry
Database: PDB / ID: 9fm1
TitleCryo-EM structure of Influenza B/Washington/02/2019 virus hemagglutinin in complex with single-domain antibody hVHH-69.
Components
  • Hemagglutinin
  • Single-domain antibody hVHH-69
KeywordsANTIVIRAL PROTEIN / hemagglutinin / single-domain antibody / 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 speciesInfluenza B virus
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsFelix, J. / Matthys, A. / Savvides, S.N. / Saelens, X.
Funding support Belgium, 3items
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, J.P.P. / Roose, K. / Nerinckx, W. / Van Buyten, B. / Fijalkowska, D. / Callewaert, N. / Savvides, S.N. / Saelens, X.
History
DepositionJun 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemagglutinin
B: Hemagglutinin
C: Hemagglutinin
D: Single-domain antibody hVHH-69
E: Single-domain antibody hVHH-69
F: Single-domain antibody hVHH-69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,48512
Polymers237,1576
Non-polymers1,3276
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14690 Å2
ΔGint-37 kcal/mol
Surface area61650 Å2
MethodPISA

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Components

#1: Protein Hemagglutinin


Mass: 65530.621 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza B virus / Gene: HA / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: A0A6B9RSJ6
#2: Antibody Single-domain antibody hVHH-69


Mass: 13521.857 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Komagataella phaffii (fungus)
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex between Influenza B/Washington/02/2019 virus hemagglutinin and single-domain antibody hVHH-69
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.27 MDa / Experimental value: YES
Source (natural)Organism: Influenza B virus
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293F
Buffer solutionpH: 7.4
Buffer component
IDConc.NameBuffer-ID
10.137 MSodium chloride1
20.0027 MPotassium Chloride1
30.01 MSodium Phosphate Dibasic1
40.0018 MPotassium Phosphate Monobasic1
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4352
Details: Images were collected at 40 degree tilt to overcome preferred orientations.

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2particle selection
2SerialEMimage acquisition
4cryoSPARC4.2CTF correction
8PHENIXmodel refinement
10cryoSPARC4.2initial Euler assignment
11cryoSPARC4.2final Euler assignment
12cryoSPARC4.2classification
13cryoSPARC4.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4124258
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 157829 / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311844
ELECTRON MICROSCOPYf_angle_d0.70416128
ELECTRON MICROSCOPYf_dihedral_angle_d12.2984251
ELECTRON MICROSCOPYf_chiral_restr0.0491854
ELECTRON MICROSCOPYf_plane_restr0.0052094

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