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- EMDB-44305: Cryo-EM structure of antibody TJ5-13 bound to H3 COBRA NG2 hemagg... -

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Basic information

Entry
Database: EMDB / ID: EMD-44305
TitleCryo-EM structure of antibody TJ5-13 bound to H3 COBRA NG2 hemagglutinin
Map dataSharpened map
Sample
  • Complex: A complex of TJ5-13 Fab bound to the H3 COBRA NG2
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: TJ5-13 Fab heavy chain
    • Protein or peptide: TJ5-13 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordshemagglutinin / antigen / antibody / Fab / VIRAL 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
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 speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsDzimianski JV / Cruz JM / Serrao VHB / DuBois RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00052 United States
CitationJournal: J Virol / Year: 2025
Title: Assessing the structural boundaries of broadly reactive antibody interactions with diverse H3 influenza hemagglutinin proteins.
Authors: John V Dzimianski / Kaito A Nagashima / Joseph M Cruz / Giuseppe A Sautto / Sara M O'Rourke / Vitor H B Serrão / Ted M Ross / Jarrod J Mousa / Rebecca M DuBois /
Abstract: Influenza virus infections are an ongoing seasonal disease burden and a persistent pandemic threat. Formulating successful vaccines remains a challenge due to accumulating mutations in circulating ...Influenza virus infections are an ongoing seasonal disease burden and a persistent pandemic threat. Formulating successful vaccines remains a challenge due to accumulating mutations in circulating strains, necessitating the development of innovative strategies to combat present and future viruses. One promising strategy for attaining greater vaccine effectiveness and longer-lasting protection is the use of computationally optimized broadly reactive antigens (COBRAs). The COBRA approach involves antigen design by generating iterative, layered consensus sequences based on current and historic viruses. Antigens designed by this process show a greater breadth of antibody-mediated protection compared to wild-type antigens, with effectiveness that often extends beyond the sequence design space of the COBRA. In particular, the use of COBRA hemagglutinin (HA) proteins has led to the discovery of broadly reactive antibodies that are suggestive of their therapeutic potential. Understanding the extent to which these antibodies are effective is key to assessing the resilience of vaccine-induced immunity to diverging influenza strains. To investigate this, we tested the binding of broadly reactive antibodies with a diverse panel of H3 HA proteins. Using cryo-electron microscopy, we defined the molecular characteristics of binding for these antibodies at the paratope-epitope interface. Through sequence and structural comparisons, we observed the correlative patterns between antibody affinity and antigen structure. These data shed light on the breadth and limitations of broadly reactive antibody responses in the context of an ever-changing landscape of influenza virus strains, yielding insights into strategies for universal vaccine design.IMPORTANCEFormulating effective influenza vaccines remains a challenge due to a constantly changing landscape of circulating viruses. This is particularly true for H3N2 viruses that undergo a high degree of antigenic drift. Several new vaccine designs can elicit broadly neutralizing antibodies that are effective against a range of influenza strains. More insight is needed, however, into how resilient these antibodies will be to future strains that evolve in the context of this selective pressure. Here, we measured the precise binding characteristics of three broadly neutralizing antibodies to 18 different hemagglutinin (HA) proteins representing almost 50 years of virus evolution. Using single-particle cryo-electron microscopy and X-ray crystallography, we determined the structural characteristics of the epitopes bound by these antibodies and identified specific amino acids that greatly impact the effectiveness of these antibodies. This provides important insights into the longevity of antibody efficacy that can help guide design choices in next-generation vaccines.
History
DepositionMar 27, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44305.png

Downloads & links

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Map

FileDownload / File: emd_44305.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 480 pix.
= 400.8 Å		0.84 Å/pix.
x 480 pix.
= 400.8 Å		0.84 Å/pix.
x 480 pix.
= 400.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.1555182 - 1.6410463
Average (Standard dev.)-0.00014501896 (±0.028283525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 400.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44305_msk_1.map
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Additional map: Unsharpened map

Fileemd_44305_additional_1.map
AnnotationUnsharpened map
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Half map: Half map B

Fileemd_44305_half_map_1.map
AnnotationHalf map B
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Half map: Half map A

Fileemd_44305_half_map_2.map
AnnotationHalf map A
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Sample components

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Entire : A complex of TJ5-13 Fab bound to the H3 COBRA NG2

EntireName: A complex of TJ5-13 Fab bound to the H3 COBRA NG2
Components
  • Complex: A complex of TJ5-13 Fab bound to the H3 COBRA NG2
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: TJ5-13 Fab heavy chain
    • Protein or peptide: TJ5-13 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: A complex of TJ5-13 Fab bound to the H3 COBRA NG2

SupramoleculeName: A complex of TJ5-13 Fab bound to the H3 COBRA NG2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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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
Molecular weightTheoretical: 62.717137 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QKIPGNDNST ATLCLGHHAV PNGTIVKTIT NDRIEVTNAT ELVQNSSIGE ICDSPHQILD GENCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCYP YDVPDYASLR SLVASSGTLE FKNESFNWTG VTQNGTSSAC IRGSSSSFFS RLNWLTHLNY T YPALNVTM ...String:
QKIPGNDNST ATLCLGHHAV PNGTIVKTIT NDRIEVTNAT ELVQNSSIGE ICDSPHQILD GENCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCYP YDVPDYASLR SLVASSGTLE FKNESFNWTG VTQNGTSSAC IRGSSSSFFS RLNWLTHLNY T YPALNVTM PNNEQFDKLY IWGVHHPGTD KDQIFLYAQS SGRITVSTKR SQQAVIPNIG SRPRIRDIPS RISIYWTIVK PG DILLINS TGNLIAPRGY FKIRSGKSSI MRSDAPIGKC KSECITPNGS IPNDKPFQNV NRITYGACPR YVKQSTLKLA TGM RNVPEK QTRGIFGAIA GFIENGWEGM VDGWYGFRHQ NSEGRGQAAD LKSTQAAIDQ INGKLNRLIG KTNEKFHQIE KEFS EVEGR IQDLEKYVED TKIDLWSYNA ELLVALENQH TIDLTDSEMN KLFEKTKKQL RENAEDMGNG CFKIYHKCDN ACIGS IRNG TYDHNVYRDE ALNNRFQIKG VEGYIPEAPR DGQAYVRKDG EWVLLSTFLG SGLNDIFEAQ KIEWHEGHHH HHH

UniProtKB: Hemagglutinin

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Macromolecule #2: TJ5-13 Fab heavy chain

MacromoleculeName: TJ5-13 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.796775 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCEASGDTFT TYSGINWVRQ APGQGLEWMG GVLPNFGSPN YAQRFQGRIT ITVDRSTSLV HMELTNLRS DDTAVYYCTE TGAYNSVGYF PYFQFRGQGT LVSVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
QVQLVQSGAE VKKPGSSVKV SCEASGDTFT TYSGINWVRQ APGQGLEWMG GVLPNFGSPN YAQRFQGRIT ITVDRSTSLV HMELTNLRS DDTAVYYCTE TGAYNSVGYF PYFQFRGQGT LVSVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC GSLVPRGSHH HH HH

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Macromolecule #3: TJ5-13 Fab light chain

MacromoleculeName: TJ5-13 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.762055 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QSVLTQPPSV SGAPGQRVTI SCTGSSSNIG ADYDVHWYQQ LPGTAPKLLI FGNNNRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSFDKSLSG SFVFGTGTKV TGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSVLTQPPSV SGAPGQRVTI SCTGSSSNIG ADYDVHWYQQ LPGTAPKLLI FGNNNRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSFDKSLSG SFVFGTGTKV TGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / 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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 13223 / Average electron dose: 45.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3186155
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 70400
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
source_name: SwissModel, initial_model_type: in silico model
source_name: Other, initial_model_type: in silico modelABodyBuilder
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 63
Output model

PDB-9b7g:
Cryo-EM structure of antibody TJ5-13 bound to H3 COBRA NG2 hemagglutinin

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