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- EMDB-45424: PN-SIA49 Fab fragment in complex with the Y2 COBRA hemagglutinin -

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Basic information

Entry
Database: EMDB / ID: EMD-45424
TitlePN-SIA49 Fab fragment in complex with the Y2 COBRA hemagglutinin
Map dataPN-SIA49 Fab fragment in complex with the Y2 COBRA hemagglutinin
Sample
  • Complex: Complex of PN-SIA49 Fab with the Y2 H1 COBRA hemagglutinin
    • Protein or peptide: Y2 COBRA HA
    • Protein or peptide: PN-SIA49 Fab heavy chain
    • Protein or peptide: PN-SIA49 Fab light chain
KeywordsAntibody / influenza / Fab / VIRAL PROTEIN
Biological speciesInfluenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsNagashima KA / Mousa JJ
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: Vaccines (Basel) / Year: 2026
Title: Extended Heterosubtypic Neutralization and Preclinical Model In Vivo Protection from Clade 2.3.4.4b H5 Influenza Virus Infection by Broadly Neutralizing Antibodies.
Authors: Valeria Caputo / Martina Libera / Yailin Campos Mota / Kaito Nagashima / Ana Maria Moreno Martin / Claudia Maria Trombetta / Francesca Dapporto / Jarrod J Mousa / Emanuele Montomoli / ...Authors: Valeria Caputo / Martina Libera / Yailin Campos Mota / Kaito Nagashima / Ana Maria Moreno Martin / Claudia Maria Trombetta / Francesca Dapporto / Jarrod J Mousa / Emanuele Montomoli / Giuseppe A Sautto / Roberta Antonia Diotti /
Abstract: : The influenza virus remains one of the most prevalent respiratory pathogens, posing significant global health and economic challenges. According to the World Health Organization, the seasonal ...: The influenza virus remains one of the most prevalent respiratory pathogens, posing significant global health and economic challenges. According to the World Health Organization, the seasonal influenza virus infects up to 1 billion people and causes up to 650,000 deaths, annually. Despite influenza vaccination is the most effective available preventive strategy, its reliance on strain predictions and yearly updates limits its effectiveness. The virus' ability to cause both epidemics and pandemics, driven by zoonotic transmissions, underscores its continuous threat. The ongoing H5N1 avian influenza outbreak is the perfect example, renewing concerns due to its ability to infect over 70 mammalian species and sporadically transmit to humans. This study aims to evaluate the protective potential of two human monoclonal antibodies against diverse and recent influenza virus strains. : PN-SIA28 and PN-SIA49 monoclonal antibodies were previously isolated from an individual undergoing seasonal influenza vaccination and with no known recent influenza virus exposure. Their breadth of recognition, neutralization, and conferred in vivo protection were assessed against multiple influenza viruses, including pre-pandemic strains. Structural analyses were performed to characterize antibody-antigen interactions for epitope identification. : Both antibodies recognize a broad range of strains and neutralize pre-pandemic avian influenza viruses, including the currently circulating H5N1 clade. Moreover, a structural analysis revealed that PN-SIA49 binds a conserved HA stem region, overlapping with epitopes recognized by other broadly neutralizing antibodies. : These findings underscore the potential of broadly neutralizing antibodies as a basis for universal influenza countermeasures against both seasonal and pandemic threats. Additionally, they provide guidance for the design of targeted vaccine strategies to steer immune responses toward broadly protective epitopes.
History
DepositionJun 19, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45424.png

Downloads & links

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Map

FileDownload / File: emd_45424.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPN-SIA49 Fab fragment in complex with the Y2 COBRA hemagglutinin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.22 Å/pix.
x 384 pix.
= 468.48 Å		1.22 Å/pix.
x 384 pix.
= 468.48 Å		1.22 Å/pix.
x 384 pix.
= 468.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.22 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.02569748 - 2.297837
Average (Standard dev.)0.0005001541 (±0.013976184)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 468.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Additional Map

Fileemd_45424_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_45424_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_45424_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 PN-SIA49 Fab with the Y2 H1 COBRA hemagglutinin

EntireName: Complex of PN-SIA49 Fab with the Y2 H1 COBRA hemagglutinin
Components
  • Complex: Complex of PN-SIA49 Fab with the Y2 H1 COBRA hemagglutinin
    • Protein or peptide: Y2 COBRA HA
    • Protein or peptide: PN-SIA49 Fab heavy chain
    • Protein or peptide: PN-SIA49 Fab light chain

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Supramolecule #1: Complex of PN-SIA49 Fab with the Y2 H1 COBRA hemagglutinin

SupramoleculeName: Complex of PN-SIA49 Fab with the Y2 H1 COBRA hemagglutinin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus

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Macromolecule #1: Y2 COBRA HA

MacromoleculeName: Y2 COBRA HA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKAILVVLLY TFTTANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVETS NSDNGTCYPG DFINYEELRE QLSSVSSFER FEIFPKTSSW PNHDSNKGVT AACPHAGAKS FYKNLIWLVK ...String:
MKAILVVLLY TFTTANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVETS NSDNGTCYPG DFINYEELRE QLSSVSSFER FEIFPKTSSW PNHDSNKGVT AACPHAGAKS FYKNLIWLVK KGNSYPKLSQ SYINDKGKEV LVLWGIHHPS TTADQQSLYQ NADAYVFVGT SRYSKKFKPE IAIRPKVRDQ EGRMNYYWTL VEPGDKITFE ATGNLVVPRY AFTMERNAGS GIIISDTPVH DCNTTCQTPE GAINTSLPFQ NVHPITIGKC PKYVKSTKLR LATGLRNVPS IQSRGLFGAI AGFIEGGWTG MVDGWYGYHH QNEQGSGYAA DLKSTQNAID KITNKVNSVI EKMNTQFTAV GKEFNHLEKR IENLNKKVDD GFLDIWTYNA ELLVLLENER TLDYHDSNVK NLYEKVRNQL KNNAKEIGNG CFEFYHKCDN TCMESVKNGT YDYPKYSEEA KLNREKIDGV GTGYIPEAPR DGQAYVRKDG EWVLLSTFLG SGLNDIFEAQ KIEWHEGHHH HHH

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Macromolecule #2: PN-SIA49 Fab heavy chain

MacromoleculeName: PN-SIA49 Fab heavy chain / type: protein_or_peptide / ID: 2 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVKLLESGGG LVQPGGSLRL SCAASGITFS SYAMSWVRQA PGKGLEWVST VNSGGGSTYY GDSVRGRFTI SRDNSKSTLY LQLNSLRAED TAIYYCAKDK GRPIFGLVTP SYYMDVWGNG TTVTVSS

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Macromolecule #3: PN-SIA49 Fab light chain

MacromoleculeName: PN-SIA49 Fab light chain / type: protein_or_peptide / ID: 3 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
ELTQSPSSLS ASVGDSVTIT CRTSERISTY LNWYQQKPGK APRLLVSGAS TLQGGVPSRF SGSGSGTAFT LTINSLQPED FATYYCQQSY STPLTFGGGT KVEIK

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 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: 110499
CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110499
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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