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- EMDB-48510: Cryo-EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoc... -

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Basic information

Entry
Database: EMDB / ID: EMD-48510
TitleCryo-EM map of H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 20D10 and CR9114
Map data
Sample
  • Complex: H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 20D10 and CR9114
    • Protein or peptide: 20D10 Heavy Chain Fab
    • Protein or peptide: 20D10 Light Chain Fab
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza / hemaglutinin / antibody-antigen complex / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 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)75N39019C00051 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 1, 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_48510.png

Downloads & links

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Map

FileDownload / File: emd_48510.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 440 pix.
= 319. Å		0.73 Å/pix.
x 440 pix.
= 319. Å		0.73 Å/pix.
x 440 pix.
= 319. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.4156619 - 0.57040364
Average (Standard dev.)-0.000040599138 (±0.016406924)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 319.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48510_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48510_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48510_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 : H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 20D10...

EntireName: H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 20D10 and CR9114
Components
  • Complex: H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 20D10 and CR9114
    • Protein or peptide: 20D10 Heavy Chain Fab
    • Protein or peptide: 20D10 Light Chain Fab
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 20D10...

SupramoleculeName: H5 HA (A/Jiangsu/NJ210/2023) in complex with monoclonal fab 20D10 and CR9114
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 280 KDa

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Macromolecule #1: 20D10 Heavy Chain Fab

MacromoleculeName: 20D10 Heavy Chain Fab / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.253739 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLQESGPGL VKPSETLSLT CTVSGGSISS YYWSWIRQPP GKGLEWIGSI YYSGSTNYNP SLKSLSIISV DTSKNQFSLK LNSVTAADT AVYYCARELA STGPLYYYYG MDVWGQGTTV TVS

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Macromolecule #2: 20D10 Light Chain Fab

MacromoleculeName: 20D10 Light Chain Fab / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.232831 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPLS LPVTPGEPAS ISCRSSQSLL HSIGYTYLDW YLQKPGQSPK LLIYLGTDRA PGVPDRFSGS GSGTDFTLKI SRVEAEDVG VYYCMQALQT PYTFGQGTKL EIK

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Macromolecule #3: Hemagglutinin HA1

MacromoleculeName: Hemagglutinin HA1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Jiangsu/NJ210/2023
Molecular weightTheoretical: 39.088605 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENIVLLLAI VNLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCDL NGVKPLILKD CSVAGWLLGN PMCDEFIRV PEWSYIVERD NPANDLCYPG SLNDYEELKH LLSRINHFEK ILIIPKSSWP NHETSLGVSA ACPYQGAPSF F RNVVWLIK ...String:
MENIVLLLAI VNLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCDL NGVKPLILKD CSVAGWLLGN PMCDEFIRV PEWSYIVERD NPANDLCYPG SLNDYEELKH LLSRINHFEK ILIIPKSSWP NHETSLGVSA ACPYQGAPSF F RNVVWLIK KDDAYPTIKI SYNNTNREDL LILWGIHHSN NAEEQTNLYK NPTTYISVGT STLNQRLVPK IATRSQVNGQ RG RMDFFWT ILKPDDAIHF ESNGNFIAPE YAYKIVKKGD STIMKSGVEY GHCNTKCQTP VGAINSSMPF HNIHPLTIGE CPK YVKSNK LVLATGLRNS PPREKRRKR

UniProtKB: Hemagglutinin

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Macromolecule #4: Hemagglutinin HA2

MacromoleculeName: Hemagglutinin HA2 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Jiangsu/NJ210/2023
Molecular weightTheoretical: 25.352949 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFGAIAGFI EGGWQGMVDG WYGYHHSNEQ GSGYAADKES TQKAIDGVTN KVNSIIDKMN TQFEAVGREF NNLERRIENL NKKMEDGFL DVWTYNAELL VLMENERTLD FHDSNVKNLY DKVRLQLRDN AKELGNGCFE FYHKCDNECM ESVRNGTYYY P QYSEEARL ...String:
GLFGAIAGFI EGGWQGMVDG WYGYHHSNEQ GSGYAADKES TQKAIDGVTN KVNSIIDKMN TQFEAVGREF NNLERRIENL NKKMEDGFL DVWTYNAELL VLMENERTLD FHDSNVKNLY DKVRLQLRDN AKELGNGCFE FYHKCDNECM ESVRNGTYYY P QYSEEARL KREEISGVGY IPEAPRDGQA YVRKDGEWVL LSTFLGSENL YFQGGSHHHH HH

UniProtKB: Hemagglutinin

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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: 12 / 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

Concentration0.56 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 44.74 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 44504
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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