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- PDB-24kr: Structural basis of influenza A virus neutralization by broadly a... -

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Basic information

Entry
Database: PDB / ID: 24kr
TitleStructural basis of influenza A virus neutralization by broadly active single-domain antibody G2.3 recognizing glycosylated epitope within hemagglutinin stem
Components
  • Heavy chain antibody G2.3-Fc
  • Hemagglutinin
KeywordsANTIVIRAL PROTEIN / hemagglutinin / influenza A / H1N1 / antibody / G2.3 / cryoEM / stem domain
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / metal ion binding
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesInfluenza A virus
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsIlyasov, I.O. / Baymukhametov, T.N. / Voronina, D.V. / Vorobiev, I.I. / Khodak, Y.A. / Burtseva, A.D. / Popov, V.O. / Sluchanko, N.N. / Shcheblyakov, D.V. / Boyko, K.M.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science FoundationNo. 23-74-30004 Russian Federation
Citation
Journal: Int J Biol Macromol / Year: 2026
Title: Structural basis of influenza A virus neutralization by broadly reactive single-domain antibody G2.3 recognizing glycosylated epitope within hemagglutinin stem domain.
Authors: Igor O Ilyasov / Daria V Voronina / Timur N Baymukhametov / Ivan I Vorobiev / Ekaterina I Ryabova / Artem A Derkaev / Ilias B Esmagambetov / Maxim M Shmarov / Yulia A Khodak / Anna D ...Authors: Igor O Ilyasov / Daria V Voronina / Timur N Baymukhametov / Ivan I Vorobiev / Ekaterina I Ryabova / Artem A Derkaev / Ilias B Esmagambetov / Maxim M Shmarov / Yulia A Khodak / Anna D Burtseva / Nikolai N Sluchanko / Konstantin M Boyko / Dmitry V Shcheblyakov / Aleksandr L Gintsburg / Vladimir O Popov / Denis Y Logunov /
Abstract: Influenza remains one of the most common and contagious respiratory infections causing around a billion cases of seasonal illness annually and five million cases of severe consequences. A recently ...Influenza remains one of the most common and contagious respiratory infections causing around a billion cases of seasonal illness annually and five million cases of severe consequences. A recently reported G2.3 antibody exhibited a potent cross-subtype activity against Group 1 influenza A viruses. Here, we shed light on the structural basis of the broad neutralizing activity of G2.3 by using cryoEM. Structural analysis of the G2.3 complex with H1 hemagglutinin revealed a partly conserved epitope located on the stem domain. The structural data were confirmed by the assessment of binding and neutralizing properties of the Fc-modified form of G2.3 with a broad panel of recombinant hemagglutinins and influenza A viruses. We demonstrated remarkably high activity of G2.3-Fc against H1N1 viral strains, which is consistent with G2.3 epitope being the most conserved within the H1 subtype, but low activity towards Group 2 of HA, which was explained by the analysis of the epitope. To suggest the mechanism of G2.3 neutralization, we compared its epitope with those of other broadly neutralizing antibodies that attack the stem domain. Finally, we obtained an escape mutant that has two mutations within the epitope and around, unseen in circulating H1 strains, allowing this mutant to elude from G2.3 and made assumption of the mechanism of such evasion.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 8, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: 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
D: Heavy chain antibody G2.3-Fc
B: Hemagglutinin
E: Heavy chain antibody G2.3-Fc
C: Hemagglutinin
F: Heavy chain antibody G2.3-Fc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,22421
Polymers322,9066
Non-polymers3,31815
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Hemagglutinin


Mass: 63447.141 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/California/04/2009(H1N1))
Gene: HA / Variant: A/California/04/2009 / Cell line (production host): CHO-S / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: C3W5S1
#2: Antibody Heavy chain antibody G2.3-Fc


Mass: 44188.168 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#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.: 15 / 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: Single-domain antibody G2.3 in complex with hemagglutinin H1
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.465 MDa / Experimental value: NO
Source (natural)Organism: Influenza A virus (A/California/04/2009(H1N1))
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: Preliminary grid screening was performed manually.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 600 nm / Cs: 0.01 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.9 sec. / Electron dose: 66 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2953
Details: Images were collected in movie-mode at 60 frames per exposure time.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Spherical aberration corrector: Microscope was modified with a CETCOR Cs corrector (CEOS GmbH).
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2PHENIX1.21.2_5419model refinement
3SerialEM4.055image acquisition
5cryoSPARC4.6.0CTF correction
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
13cryoSPARC4.6.03D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 3486535
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 96191 / Symmetry type: POINT

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