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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: To Be Published
Title: Human Monoclonal Antibodies that Target Clade 2.3.4.4b H5N1 Hemagglutinin
Authors: Pena Alzua G / Leon AN / Brouwer PJM / Yellin T / Bhavsar D / Loganathan M / Bushfield K / Marizzi C / Rodriguez AJ / Han J / Webby R / Ward AB / Duty JA / Krammer F
History
DepositionJan 1, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 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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