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- EMDB-48684: Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex ... -

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Entry
Database: EMDB / ID: EMD-48684
TitleNegative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12C11
Map dataNegative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12C11
Sample
  • Complex: Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12C11
Keywordsinfluenza / hemagglutinin / H5 / monoclonal / complex / fab complex / viral fusion protein / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsLeon AN / Brouwer PJM / Rodriguez AJ / Han J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: Nat Commun / Year: 2025
Title: Human monoclonal antibodies that target clade 2.3.4.4b H5N1 hemagglutinin.
Authors: Garazi Peña Alzua / André Nicolás León / Temima Yellin / Disha Bhavsar / Madhumathi Loganathan / Kaitlyn Bushfield / Philip J M Brouwer / Alesandra J Rodriguez / Trushar Jeevan / Richard ...Authors: Garazi Peña Alzua / André Nicolás León / Temima Yellin / Disha Bhavsar / Madhumathi Loganathan / Kaitlyn Bushfield / Philip J M Brouwer / Alesandra J Rodriguez / Trushar Jeevan / Richard Webby / Christine Marizzi / Julianna Han / Andrew B Ward / J Andrew Duty / Florian Krammer /
Abstract: The highly pathogenic avian influenza H5N1 virus clade 2.3.4.4b has been spreading globally since 2022, causing mortality and morbidity in domestic and wild birds, as well as in mammals, which ...The highly pathogenic avian influenza H5N1 virus clade 2.3.4.4b has been spreading globally since 2022, causing mortality and morbidity in domestic and wild birds, as well as in mammals, which underscores its potential to cause a pandemic. Here, we generate a panel of anti-hemagglutinin (HA) human monoclonal antibodies (mAbs) against the H5 protein of clade 2.3.4.4b. To develop human chimeric antibodies, H2L2 Harbor Mice®, which express human immunoglobulin germline genes, were immunized with H5 and N1 recombinant proteins from A/mallard/New York/22-008760-007- original/2022 H5N1 virus. Through hybridoma technology, sixteen fully human mAbs are generated, most of which show cross-reactivity against H5 proteins from different clade 2.3.4.4 virus variants. Fourteen out of the sixteen mAbs neutralize the virus in vitro. The mAbs with the strongest hemagglutination inhibition activity also demonstrate greater neutralizing capacity and show increased protective effects in vivo when administered prophylactically or therapeutically in a murine H5N1 challenge model. Using cryo-electron microscopy, we identify a cross-clonotype conserved motif that bound a hydrophobic groove on the head domain of H5 HA. Akin to mAbs against severe acute respiratory syndrome coronavirus 2 during the coronavirus 2019 pandemic, these mAbs could serve as treatments in case of a widespread H5N1 epidemic or pandemic.
History
DepositionJan 16, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48684.png

Downloads & links

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Map

FileDownload / File: emd_48684.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12C11
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.06 Å/pix.
x 208 pix.
= 428.48 Å		2.06 Å/pix.
x 208 pix.
= 428.48 Å		2.06 Å/pix.
x 208 pix.
= 428.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0163
Minimum - Maximum-0.033917587 - 0.07263235
Average (Standard dev.)0.00002210215 (±0.0033592482)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 428.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Negative stain EM half map B of H5...

Fileemd_48684_half_map_1.map
AnnotationNegative stain EM half map B of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12C11
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain EM half map A of H5...

Fileemd_48684_half_map_2.map
AnnotationNegative stain EM half map A of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12C11
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex ...

EntireName: Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12C11
Components
  • Complex: Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12C11

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Supramolecule #1: Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex ...

SupramoleculeName: Negative stain EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 12C11
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 280 KDa

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.015 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: 2% w/v uranyl formate

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6e7g

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 2256
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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