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- EMDB-67557: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3BG3 IgG -

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Basic information

Entry
Database: EMDB / ID: EMD-67557
TitleCryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3BG3 IgG
Map data
Sample
  • Complex: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3BG3 IgG
    • Protein or peptide: The heavy chain of 3BG3 IgG
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: The light chain of 3BG3 IgG
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHemagglutinin / Antibody Fab fragment / Complex / VIRAL PROTEIN/IMMUNE SYSTEM / VIRUS
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
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 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsNiu C / Liu B / Li Z / Xiong X
Funding support China, 8 items
OrganizationGrant numberCountry
Other government2021YFA1300903
National Natural Science Foundation of China (NSFC)82341085 China
Other governmentEKPG21-06
Other governmentSRPG22-002
Other government2021A1515011289
Other government2023B1212060050
Other government2023B1212120009
Other governmentGIBHBRP24-02
CitationJournal: To Be Published
Title: A broadly neutralizing monoclonal antibody targeting a conserved non-RBS epitope on hemagglutinins of emerging and historical H5Nx influenza viruses
Authors: Niu X / Liang H / Niu C / Cheng Y / Liew K / Zheng Z / Liu B / Li Z / Feng H / Tan Y / Xiong X / Chen L
History
DepositionDec 6, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67557.png

Downloads & links

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Map

FileDownload / File: emd_67557.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å		1.32 Å/pix.
x 256 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.6803155 - 2.8654256
Average (Standard dev.)0.000749964 (±0.060822904)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67557_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_67557_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 : CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3BG3 IgG

EntireName: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3BG3 IgG
Components
  • Complex: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3BG3 IgG
    • Protein or peptide: The heavy chain of 3BG3 IgG
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: The light chain of 3BG3 IgG
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3BG3 IgG

SupramoleculeName: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to 3BG3 IgG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus

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Macromolecule #1: The heavy chain of 3BG3 IgG

MacromoleculeName: The heavy chain of 3BG3 IgG / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 49.368484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LAKPSETLTL TCAVSGGSIG EVYFWNWIRQ SPGKGLEWIG FIRGSGDRTS YNPSLKSRVS ISTDTSKSHF SLTLSPLTA ADTAVYYCAR EMVESGVTWL DHWGQGHLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QVQLQESGPG LAKPSETLTL TCAVSGGSIG EVYFWNWIRQ SPGKGLEWIG FIRGSGDRTS YNPSLKSRVS ISTDTSKSHF SLTLSPLTA ADTAVYYCAR EMVESGVTWL DHWGQGHLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HTCPPCPAPE LL GGPSVFL FPPKPKDTLM ISRTPEVTCV VVDVSHEDPE VKFNWYVDGV EVHNAKTKPR EEQYNSTYRV VSVLTVLHQD WLN GKEYKC KVSNKALPAP IEKTISKAKG QPREPQVYTL PPSRDELTKN QVSLTCLVKG FYPSDIAVEW ESNGQPENNY KTTP PVLDS DGSFFLYSKL TVDKSRWQQG NVFSCSVMHE ALHNHYTQKS LSLSPGK

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Macromolecule #2: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: strain A/Texas/37/2024 H5N1
Molecular weightTheoretical: 62.840508 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CYPGSLNDYE ELKHMLSRIN HFEKIQIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN ...String:
DQICIGYHAN NSTEQVDTIM EKNVTVTHAQ DILEKTHNGK LCDLNGVKPL ILKDCSVAGW LLGNPMCDEF IRVPEWSYIV ERANPANDL CYPGSLNDYE ELKHMLSRIN HFEKIQIIPK SSWPNHETSL GVSAACPYQG APSFFRNVVW LIKKNDAYPT I KISYNNTN REDLLILWGI HHSNNAEEQT NLYKNPITYI SVGTSTLNQR LAPKIATRSQ VNGQRGRMDF FWTILKPDDA IH FESNGNF IAPEYAYKIV KKGDSTIMKS GVEYGHCNTK CQTPVGAINS SMPFHNIHPL TIGECPKYVK SNKLVLATGL RNS PLREKR RKRGLFGAIA GFIEGGWQGM VDGWYGYHHS NEQGSGYAAD KESTQKAIDG VTNKVNSIID KMNTQFEAVG REFN NLERR IENLNKKMED GFLDVWTYNA ELLVLMENER TLDFHDSNVK NLYDKVRLQL RDNAKELGNG CFEFYHKCDN ECMES VRNG TYDYPQYSEE ARLKREEISG SGRENLYFQG GGGSGYIPEA PRDGQAYVRK DGEWVLLSTF LGHHHHHH

UniProtKB: Hemagglutinin

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Macromolecule #3: The light chain of 3BG3 IgG

MacromoleculeName: The light chain of 3BG3 IgG / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 22.420822 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QAGLTQPPSV SVSLGQTAKI TCSGDKLATN YAHWYRQKPG QAPVLVLYKG NERPSGTPER FSGSSSGTTV TLTISGAQAE DEADYYCYS GFDNKLFGGG TRLTVLGQPK AAPSVTLFPP SSEELQANKA TLVCLISDFY PGAVTVAWKA DSSPVKAGVE T TTPSKQSN ...String:
QAGLTQPPSV SVSLGQTAKI TCSGDKLATN YAHWYRQKPG QAPVLVLYKG NERPSGTPER FSGSSSGTTV TLTISGAQAE DEADYYCYS GFDNKLFGGG TRLTVLGQPK AAPSVTLFPP SSEELQANKA TLVCLISDFY PGAVTVAWKA DSSPVKAGVE T TTPSKQSN NKYAASSYLS LTPEQWKSHR SYSCQVTHEG STVEKTVAPT ECS

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 9 / 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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9ekf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 120969
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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