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- EMDB-47241: Cryo-EM structure of hemagglutinin H5 A/Texas/37/2024 in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-47241
TitleCryo-EM structure of hemagglutinin H5 A/Texas/37/2024 in complex with LSTa and antibody CR9114
Map data
Sample
  • Complex: Hemagglutinin H5 A/Texas/37/2024 homotrimer bound to LSTa and CR9114 Fab
    • Complex: CR9114 Fab
      • Protein or peptide: CR9114 Fab light chain
      • Protein or peptide: CR9114 Fab Fab heavy chain
    • Complex: Hemagglutinin
      • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHemagglutinin / Sialic Acid Complex / Antibody / VIRAL PROTEIN / H5N1 / 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
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsFernandez-Quintero ML / Han J / Rodriguez AJ / 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: 2024
Title: A single mutation in dairy cow-associated H5N1 viruses increases receptor binding breadth.
Authors: Marina R Good / Monica L Fernández-Quintero / Wei Ji / Alesandra J Rodriguez / Julianna Han / Andrew B Ward / Jenna J Guthmiller /
Abstract: Clade 2.3.4.4b H5N1 is causing an unprecedented outbreak in dairy cows in the United States. To understand if recent H5N1 viruses are changing their receptor use, we screened recombinant ...Clade 2.3.4.4b H5N1 is causing an unprecedented outbreak in dairy cows in the United States. To understand if recent H5N1 viruses are changing their receptor use, we screened recombinant hemagglutinin (HA) from historical and recent 2.3.4.4b H5N1 viruses for binding to distinct glycans bearing terminal sialic acids using a glycan microarray. We find that H5 from A/Texas/37/2024, an isolate from the dairy cow outbreak, has increased binding breadth to core glycans bearing terminal α2,3 sialic acids, the avian receptor, compared to historical and recent 2.3.4.4b H5N1 viruses. We do not observe any binding to α2,6 sialic acids, the receptor used by human seasonal influenza viruses. Using molecular dynamics and a cryo-EM structure of A/Texas/37/2024 H5, we show A/Texas/37/2024 H5 is more flexible within the receptor-binding site compared to a 2.3.4.4b H5 from 2022. We identify a single mutation outside of the receptor binding site, T199I, is responsible for increased binding breadth, as it increases receptor binding site flexibility. Together, these data show recent H5N1 viruses are evolving increased receptor binding breadth which could impact the host range and cell types infected with H5N1.
History
DepositionOct 9, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47241.png

Downloads & links

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Map

FileDownload / File: emd_47241.map.gz / Format: CCP4 / Size: 512 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 512 pix.
= 371.2 Å		0.73 Å/pix.
x 512 pix.
= 371.2 Å		0.73 Å/pix.
x 512 pix.
= 371.2 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: 0.173
Minimum - Maximum-1.0164186 - 1.3276434
Average (Standard dev.)0.000024404866 (±0.022767756)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 371.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47241_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47241_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 : Hemagglutinin H5 A/Texas/37/2024 homotrimer bound to LSTa and CR9...

EntireName: Hemagglutinin H5 A/Texas/37/2024 homotrimer bound to LSTa and CR9114 Fab
Components
  • Complex: Hemagglutinin H5 A/Texas/37/2024 homotrimer bound to LSTa and CR9114 Fab
    • Complex: CR9114 Fab
      • Protein or peptide: CR9114 Fab light chain
      • Protein or peptide: CR9114 Fab Fab heavy chain
    • Complex: Hemagglutinin
      • Protein or peptide: Hemagglutinin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Hemagglutinin H5 A/Texas/37/2024 homotrimer bound to LSTa and CR9...

SupramoleculeName: Hemagglutinin H5 A/Texas/37/2024 homotrimer bound to LSTa and CR9114 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: CR9114 Fab

SupramoleculeName: CR9114 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Hemagglutinin

SupramoleculeName: Hemagglutinin / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: CR9114 Fab light chain

MacromoleculeName: CR9114 Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.482556 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
SALTQPPAVS GTPGQRVTIS CSGSDSNIGR RSVNWYQQFP GTAPKLLIYS NDQRPSVVPD RFSGSKSGTS ASLAISGLQS EDEAEYYCA AWDDSLKGAV FGGGTQLTVL G

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Macromolecule #2: CR9114 Fab Fab heavy chain

MacromoleculeName: CR9114 Fab Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.911277 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLVQSGAE VKKPGSSVKV SCKSSGGTSN NYAISWVRQA PGQGLDWMGG ISPIFGSTAY AQKFQGRVTI SADIFSNTAY MELNSLTSE DTAVYFCARH GNYYYYSGMD VWGQGTTVTV S

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Macromolecule #3: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 65.198391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MENIVLLLAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCDL NGVKPLILKD CSVAGWLLGN PMCDEFIRV PEWSYIVERA NPANDLCYPG SLNDYEELKH MLSRINHFEK IQIIPKSSWP NHETSLGVSA ACPYQGAPSF F RNVVWLIK ...String:
MENIVLLLAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCDL NGVKPLILKD CSVAGWLLGN PMCDEFIRV PEWSYIVERA NPANDLCYPG 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 PLREKRRKRG LFGAIAGFIE GGWQGMVDGW YGYHHSNEQG SGYAADKEST QKAIDGVTNK VNSI IDKMN TQFEAVGREF NNLERRIENL NKKMEDGFLD VWTYNAELLV LMENERTLDF HDSNVKNLYD KVRLQLRDNA KELGN GCFE FYHKCDNECM ESVRNGTYDY PQYSEEARLK REEISGSGYI PEAPRDGQAY VRKDGEWVLL STFLGSGLND IFEAQK IEW HEGHHHHHH

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: 15 / 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

Concentration0.7 mg/mL
BufferpH: 7.4 / Details: TBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.
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 IV (4k x 4k) / Number grids imaged: 1 / Number real images: 4922 / Average electron dose: 41.63 e/Å2
Electron beamAcceleration voltage: 200 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: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: Ab initio reconstruction
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v.4.5.3) / Number images used: 260000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
ChainPDB ID
chain_id: A, source_name: AlphaFold, initial_model_type: in silico model
chain_id: B, source_name: AlphaFold, initial_model_type: in silico model
chain_id: C, source_name: AlphaFold, initial_model_type: in silico model
chain_id: L, source_name: PDB, initial_model_type: experimental model

4fqh

chain_id: H, source_name: PDB, initial_model_type: experimental model

4fqh

Output model

PDB-9dwe:
Cryo-EM structure of hemagglutinin H5 A/Texas/37/2024 in complex with LSTa and antibody CR9114

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