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- EMDB-48518: Cryo-EM structure of hemagglutinin H5N1 in complex with Fab 310-7D11 -

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Basic information

Entry
Database: EMDB / ID: EMD-48518
TitleCryo-EM structure of hemagglutinin H5N1 in complex with Fab 310-7D11
Map data
Sample
  • Complex: Complex between hemagglutinin H5N1 and Fab 310-7D11
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: 310-7D11 Fab Heavy chain
    • Protein or peptide: 310-7D11 Fab Light chain
KeywordsHighly pathogenic avian influenza / hemagglutinin H5N1 / bird flu / VIRAL PROTEIN
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 speciesInfluenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsMalla TN / Tsybovsky Y / Zhou T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Microbiol / Year: 2025
Title: Cross-neutralizing and potent human monoclonal antibodies against historical and emerging H5Nx influenza viruses.
Authors: Alexandra A Abu-Shmais / Gray Freeman / Adrian Creanga / Matthew J Vukovich / Tek Malla / Grace E Mantus / Geoffrey D Shimberg / Rebecca A Gillespie / Vanessa Guerra Canedo / Bernadeta ...Authors: Alexandra A Abu-Shmais / Gray Freeman / Adrian Creanga / Matthew J Vukovich / Tek Malla / Grace E Mantus / Geoffrey D Shimberg / Rebecca A Gillespie / Vanessa Guerra Canedo / Bernadeta Dadonaite / Megan D Rodgers / Ankita J Chopde / Elizabeth Bardwil-Lugones / Tatsiana Bylund / Amy R Henry / Jesmine Roberts-Torres / Timothy S Johnston / Sarah Smith / Eun Sung Yang / Cheng Cheng / Emma L Walker / Michelle Ravichandran / Ingelise J Gordon / Tejaswi S Dittakavi / Douglas S Reed / Theodore C Pierson / Lesia Dropulic / Jesse D Bloom / Yaroslav Tsybovsky / Eli A Boritz / Daniel C Douek / Tongqing Zhou / Masaru Kanekiyo / Sarah F Andrews /
Abstract: Highly pathogenic avian influenza H5Nx viruses are an emerging threat for global health, especially clade 2.3.4.4b H5N1 virus which causes panzootic infections. Here we describe the isolation and ...Highly pathogenic avian influenza H5Nx viruses are an emerging threat for global health, especially clade 2.3.4.4b H5N1 virus which causes panzootic infections. Here we describe the isolation and characterization of broadly cross-neutralizing monoclonal antibodies (mAbs) against diverse H5Nx viruses from individuals who received a monovalent H5N1 vaccine 15 years ago. By screening over 500 mAbs, we identified 5 mAbs that neutralized the majority of H5 clades including 2.3.4.4b and target three distinct conserved epitopes within the HA globular head. Cryo-electron microscopy structures of these mAbs in complex with HA, deep mutational scanning and neutralization escape studies define the sites of vulnerability of H5 HA. These mAbs mediated stronger prophylactic protection against clade 2.3.4.4b H5N1 infection in mice than the best-in-class mAb targeting the HA stem. Our study identified several highly potent broadly neutralizing H5 mAbs from humans that either alone or in combination provide a pragmatic pandemic preparedness option against the threat of panzootic H5N1 influenza.
History
DepositionJan 2, 2025-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48518.png

Downloads & links

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Map

FileDownload / File: emd_48518.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 400 pix.
= 400. Å		1 Å/pix.
x 400 pix.
= 400. Å		1 Å/pix.
x 400 pix.
= 400. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.226
Minimum - Maximum-1.6658876 - 2.121624
Average (Standard dev.)-0.001001443 (±0.035267726)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 400.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48518_msk_1.map
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AxesZYX

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Additional map: Map sharpened by deepEmhancer

Fileemd_48518_additional_1.map
AnnotationMap sharpened by deepEmhancer
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Additional map: Unsharpened map

Fileemd_48518_additional_2.map
AnnotationUnsharpened map
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Half map: #2

Fileemd_48518_half_map_1.map
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Half map: #1

Fileemd_48518_half_map_2.map
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Sample components

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Entire : Complex between hemagglutinin H5N1 and Fab 310-7D11

EntireName: Complex between hemagglutinin H5N1 and Fab 310-7D11
Components
  • Complex: Complex between hemagglutinin H5N1 and Fab 310-7D11
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: 310-7D11 Fab Heavy chain
    • Protein or peptide: 310-7D11 Fab Light chain

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Supramolecule #1: Complex between hemagglutinin H5N1 and Fab 310-7D11

SupramoleculeName: Complex between hemagglutinin H5N1 and Fab 310-7D11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus / Strain: H5N1
Molecular weightTheoretical: 268.68 KDa

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Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 38.59007 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENIVLLLAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCDL NGVKPLILKD CSVAGWLLGN PMCDEFIRV PEWSYIVERA NPANDLCFPG SLNDYEELKH MLSRINHFEK IQIIPKSSWP NHETSLGVSA ACPYQGAPSF F RNVVWLIK ...String:
MENIVLLLAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCDL NGVKPLILKD CSVAGWLLGN PMCDEFIRV PEWSYIVERA NPANDLCFPG SLNDYEELKH MLSRINHFEK IQIIPKSSWP NHETSLGVSA ACPYQGAPSF F RNVVWLIK KNDAYPTIKI SYNNTNREDL LILWGIHHSN NAEEQTNLYK NPITYISVGT STLNQRLAPK IATRSQVNGQ RG RMDFFWT ILKPDDAIHF ESNGNFIAPE YAYKIVKKGD STIMKSGVEY GHCNTKCQTP VGAINSSMPF HNIHPLTIGE CPK YVKSNK LVLATGLRNS PLREKR

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 26.166805 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFGAIAGFI EGGWQGMVDG WYGYHHSNEQ GSGYAADKES TQKAIDGVTN KVNSIIDKMN TQFEAVGREF NNLERRIENL NKKMEDGFL DVWTYNAELL VLMENERTLD FHDSNVKNLY DKVRLQLRDN AKELGNGCFE FYHKCDNECM ESVRNGTYDY P QYSEEARL ...String:
GLFGAIAGFI EGGWQGMVDG WYGYHHSNEQ GSGYAADKES TQKAIDGVTN KVNSIIDKMN TQFEAVGREF NNLERRIENL NKKMEDGFL DVWTYNAELL VLMENERTLD FHDSNVKNLY DKVRLQLRDN AKELGNGCFE FYHKCDNECM ESVRNGTYDY P QYSEEARL KREEISGSGY IPEAPRDGQA YVRKDGEWVL LSTFLGSGLN DIFEAQKIEW HEGHHHHHH

UniProtKB: Hemagglutinin

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Macromolecule #3: 310-7D11 Fab Heavy chain

MacromoleculeName: 310-7D11 Fab Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.882533 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG VVQPGRSLRV SCAASGFIFS NYGMHWVRQA PGKGLEWVAL TWYDGRNKYY ADSVKGRFTI SRDNSKNTLY LQMNSLRAE DTAVYYCARD GFPNCISATC GYAMDVWGQG TTVTVSS

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Macromolecule #4: 310-7D11 Fab Light chain

MacromoleculeName: 310-7D11 Fab Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.113605 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DTVMTQSPLS LPVTPGEPAS ISCRSSQSLL HSNGYNYLEW YLQKPGQSPQ LLIYLGSIRA SGVPDRLSGS GSGTDFTLKI SRVEAEDVG VYYCMQGLET PFTFGPGTKV EIK

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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: 7.4 / Details: 10 mM HEPES, 150 mM NaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM (ver. 4.09)
Image recordingFilm or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1975843
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1461821
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: Coot
RefinementSpace: REAL
Output model

PDB-9mqa:
Cryo-EM structure of hemagglutinin H5N1 in complex with Fab 310-7D11

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