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- EMDB-47024: TJ5-1 Fab in complex with NG2 COBRA hemagglutinin -

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Basic information

Entry
Database: EMDB / ID: EMD-47024
TitleTJ5-1 Fab in complex with NG2 COBRA hemagglutinin
Map dataTJ5-1 Fab in complex with NG2 COBRA hemagglutinin
Sample
  • Complex: Complex of TJ5-1 Fab fragment with NG2 COBRA hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: TJ5-1 heavy chain Fab fragment
    • Protein or peptide: TJ5-1 light chain Fab fragment
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntibody / Fab / hemagglutinin / COBRA / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
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: 3.24 Å
AuthorsNagashima K / Mousa J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) 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
DepositionSep 16, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47024.png

Downloads & links

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Map

FileDownload / File: emd_47024.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTJ5-1 Fab in complex with NG2 COBRA hemagglutinin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 384 pix.
= 419.712 Å		1.09 Å/pix.
x 384 pix.
= 419.712 Å		1.09 Å/pix.
x 384 pix.
= 419.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.093 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.6539057 - 2.25211
Average (Standard dev.)0.000034686134 (±0.032460026)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 419.71204 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_47024_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_47024_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of TJ5-1 Fab fragment with NG2 COBRA hemagglutinin

EntireName: Complex of TJ5-1 Fab fragment with NG2 COBRA hemagglutinin
Components
  • Complex: Complex of TJ5-1 Fab fragment with NG2 COBRA hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: TJ5-1 heavy chain Fab fragment
    • Protein or peptide: TJ5-1 light chain Fab fragment
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of TJ5-1 Fab fragment with NG2 COBRA hemagglutinin

SupramoleculeName: Complex of TJ5-1 Fab fragment with NG2 COBRA hemagglutinin
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: 64.499406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTIIALSYI LCLVFAQKIP GNDNSTATLC LGHHAVPNGT IVKTITNDRI EVTNATELVQ NSSIGEICDS PHQILDGENC TLIDALLGD PQCDGFQNKK WDLFVERSKA YSNCYPYDVP DYASLRSLVA SSGTLEFKNE SFNWTGVTQN GTSSACIRGS S SSFFSRLN ...String:
MKTIIALSYI LCLVFAQKIP GNDNSTATLC LGHHAVPNGT IVKTITNDRI EVTNATELVQ NSSIGEICDS PHQILDGENC TLIDALLGD PQCDGFQNKK WDLFVERSKA YSNCYPYDVP DYASLRSLVA SSGTLEFKNE SFNWTGVTQN GTSSACIRGS S SSFFSRLN WLTHLNYTYP ALNVTMPNNE QFDKLYIWGV HHPGTDKDQI FLYAQSSGRI TVSTKRSQQA VIPNIGSRPR IR DIPSRIS IYWTIVKPGD ILLINSTGNL IAPRGYFKIR SGKSSIMRSD APIGKCKSEC ITPNGSIPND KPFQNVNRIT YGA CPRYVK QSTLKLATGM RNVPEKQTRG IFGAIAGFIE NGWEGMVDGW YGFRHQNSEG RGQAADLKST QAAIDQINGK LNRL IGKTN EKFHQIEKEF SEVEGRIQDL EKYVEDTKID LWSYNAELLV ALENQHTIDL TDSEMNKLFE KTKKQLRENA EDMGN GCFK IYHKCDNACI GSIRNGTYDH NVYRDEALNN RFQIKGVEGY IPEAPRDGQA YVRKDGEWVL LSTFLGSGLN DIFEAQ KIE WHEGHHHHHH

UniProtKB: Hemagglutinin

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Macromolecule #2: TJ5-1 heavy chain Fab fragment

MacromoleculeName: TJ5-1 heavy chain Fab fragment / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.931521 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVQSGAE VKKPGASVKV SCKASGYTFT GFYLHWVRQA PGQGLEWMGW INPHSGDTDF AQKFQGKVTM TRDTSSNTVY MDVNRLTSD DTAVYYCVKN DIVLGMGVWG QGTTVIVSS

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Macromolecule #3: TJ5-1 light chain Fab fragment

MacromoleculeName: TJ5-1 light chain Fab fragment / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.667729 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSV SGAPGQRVTI SCTGSSSNIG AGYNVYWFQQ LPPTAPKLLN YGDNNRPSGV PDRFSASKSG TSASLAITGL QAEDEAEYY CQSYDSSLNA YVFGTGTKVT VL

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.216 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3044243
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6wzt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 248400
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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