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- EMDB-69590: Structural basis of influenza A virus neutralization by broadly a... -

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Basic information

Entry
Database: EMDB / ID: EMD-69590
TitleStructural basis of influenza A virus neutralization by broadly active single-domain antibody G2.3 recognizing glycosylated epitope within hemagglutinin stem
Map data
Sample
  • Complex: Single-domain antibody G2.3 in complex with hemagglutinin H1
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Heavy chain antibody G2.3-Fc
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshemagglutinin / influenza A / H1N1 / antibody / G2.3 / cryoEM / stem domain / ANTIVIRAL PROTEIN
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 (A/California/04/2009(H1N1)) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsIlyasov IO / Baymukhametov TN / Voronina DV / Vorobiev II / Khodak YA / Burtseva AD / Popov VO / Sluchanko NN / Shcheblyakov DV / Boyko KM
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science FoundationNo. 23-74-30004 Russian Federation
CitationJournal: 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, 2026-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_69590.png

Downloads & links

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Map

FileDownload / File: emd_69590.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 300 pix.
= 261. Å		0.87 Å/pix.
x 300 pix.
= 261. Å		0.87 Å/pix.
x 300 pix.
= 261. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.039
Minimum - Maximum-0.08559589 - 0.2010555
Average (Standard dev.)0.0003993679 (±0.0064564226)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 261.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_69590_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_69590_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Single-domain antibody G2.3 in complex with hemagglutinin H1

EntireName: Single-domain antibody G2.3 in complex with hemagglutinin H1
Components
  • Complex: Single-domain antibody G2.3 in complex with hemagglutinin H1
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Heavy chain antibody G2.3-Fc
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Single-domain antibody G2.3 in complex with hemagglutinin H1

SupramoleculeName: Single-domain antibody G2.3 in complex with hemagglutinin H1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Influenza A virus (A/California/04/2009(H1N1))
Molecular weightTheoretical: 465 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 A virus (A/California/04/2009(H1N1))
Molecular weightTheoretical: 63.447141 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MKAILVVLLY TFATANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLST ASSWSYIVET PSSDNGTCYP GDFIDYEELR EQLSSVSSFE RFEIFPKTSS WPNHDSNKGV TAACPHAGAK S FYKNLIWL ...String:
MKAILVVLLY TFATANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLST ASSWSYIVET PSSDNGTCYP GDFIDYEELR EQLSSVSSFE RFEIFPKTSS WPNHDSNKGV TAACPHAGAK S FYKNLIWL VKKGNSYPKL SKSYINDKGK EVLVLWGIHH PSTSADQQSL YQNADTYVFV GSSRYSKKFK PEIAIRPKVR DQ EGRMNYY WTLVEPGDKI TFEATGNLVV PRYAFAMERN AGSGIIISDT PVHDCNTTCQ TPKGAINTSL PFQNIHPITI GKC PKYVKS TKLRLATGLR NIPSIQSRGL FGAIAGFIEG GWTGMVDGWY GYHHQNEQGS GYAADLKSTQ NAIDEITNKV NSVI EKMNT QFTAVGKEFN HLEKRIENLN KKVDDGFLDI WTYNAELLVL LENERTLDYH DSNVKNLYEK VRSQLKNNAK EIGNG CFEF YHKCDNTCME SVKNGTYDYP KYSEEAKLNR EEIDSGGGGR LVPRGSPGSG YIPEAPRDGQ AYVRKDGEWV LLSTFL GHH HHHH

UniProtKB: Hemagglutinin

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Macromolecule #2: Heavy chain antibody G2.3-Fc

MacromoleculeName: Heavy chain antibody G2.3-Fc / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.188168 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MLGPCMLLLL LLLGLRLQLS LGEVQLVESG GGLVQAGGSL RLSCAASGRI FRTYDMGWYR QAPGKEREFV ARISWSGGST NYADFVKGR FTISKDSAKN TVYLQMNSLK PEDTAMYFCN ADPSSVVGAI GAGYVYWGQG TQVTVSSEPK TPKPQPQPQP Q PQPNPTTE ...String:
MLGPCMLLLL LLLGLRLQLS LGEVQLVESG GGLVQAGGSL RLSCAASGRI FRTYDMGWYR QAPGKEREFV ARISWSGGST NYADFVKGR FTISKDSAKN TVYLQMNSLK PEDTAMYFCN ADPSSVVGAI GAGYVYWGQG TQVTVSSEPK TPKPQPQPQP Q PQPNPTTE SKCPKCPAPE LLGGPAPELL GGPSVFLFPP KPKDTLMISR TPEVTCVVVD VSHEDPEVKF NWYVDGVEVH NA KTKPREE QYNSTYRVVS VLTVLHQDWL NGKEYKCKVS NKALPAPIEK TISKAKGQPR EPQVYTLPPS REEMTKNQVS LTC LVKGFY PSDIAVEWES NGQPENNYKT TPPVLDSDGS FFLYSKLTVD KSRWQQGNVF SCSVMHEALH NHYTQKSLSL SPGK

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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: 15 / 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: 7.6
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a CETCOR Cs corrector (CEOS GmbH).
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 2953 / Average exposure time: 3.9 sec. / Average electron dose: 66.0 e/Å2
Details: Images were collected in movie-mode at 60 frames per exposure time.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 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: 3486535
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: NONE
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 96191
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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