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- EMDB-48120: CryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab 65C6 and... -

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Basic information

Entry
Database: EMDB / ID: EMD-48120
TitleCryoEM structure of H5N1 A/Texas/37/2024 HA bound to Fab 65C6 and an auto glycan occupying the receptor-binding site
Map data
Sample
  • Complex: Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with antibody
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Fab 65C6 Heavy Chain
    • Protein or peptide: Fab 65C6 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsH5N1 / antibody / influenza / VIRAL PROTEIN
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsMorano NC / Shapiro L / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
Citation
Journal: Structure / Year: 2025
Title: Structure of a zoonotic H5N1 hemagglutinin reveals a receptor-binding site occupied by an auto-glycan.
Authors: Nicholas C Morano / Yicheng Guo / Jordan E Becker / Zhiteng Li / Jian Yu / David D Ho / Lawrence Shapiro / Peter D Kwong /
Abstract: Highly pathogenic avian influenza has spilled into many mammals, most notably cows and poultry, with several dozen human breakthrough infections. Zoonotic crossovers, with hemagglutinins mutated to ...Highly pathogenic avian influenza has spilled into many mammals, most notably cows and poultry, with several dozen human breakthrough infections. Zoonotic crossovers, with hemagglutinins mutated to enhance viral ability to use human α2-6-linked sialic acid receptors versus avian α2-3-linked ones, highlight the pandemic risk. To gain insight into these crossovers, we determined the cryoelectron microscopy (cryo-EM) structure of the hemagglutinin from the zoonotic H5N1 A/Texas/37/2024 strain (clade 2.3.4.4b) in complex with a previously reported neutralizing antibody. Surprisingly, we found that the receptor-binding site of this H5N1 hemagglutinin was already occupied by an α2-3-linked sialic acid and that this glycan emanated from asparagine N169 of a neighboring protomer on hemagglutinin itself. This structure thus highlights recognition by influenza hemagglutinin of an "auto"-α2-3-linked sialic acid from N169, an N-linked glycan conserved in 95% of H5 strains, and adds "auto-glycan recognition," which may play a role in viral dispersal, to the complexities surrounding H5N1 zoonosis.
#1: Journal: Biorxiv / Year: 2024
Title: Structure of a zoonotic H5N1 hemagglutinin reveals a receptor-binding site occupied by an auto-glycan
Authors: Morano NC / Guo Y / Becker JE / Li Z / Yu J / Ho DD / Shapiro L / Kwong PD
History
DepositionDec 2, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48120.png

Downloads & links

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Map

FileDownload / File: emd_48120.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-2.06471 - 2.8409753
Average (Standard dev.)-0.00029518842 (±0.052136417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48120_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48120_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 : Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with antibody

EntireName: Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with antibody
Components
  • Complex: Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with antibody
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Fab 65C6 Heavy Chain
    • Protein or peptide: Fab 65C6 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with antibody

SupramoleculeName: Complex of Hemagglutinin from H5N1 HA A/Texas/37/2024 with antibody
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 360 KDa

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 65.58575 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 PLRRRRRRGL FGAIAGFIEG GWQGMVDGWY GYHHSNEQGS GYAADKESTQ KAIDGVTNKV NSII DKMNT QFEAVGREFN NLERRIENLN KKMEDGFLDV WTYNAELLVL MENERTLDFH DSNVKNLYDK VRLQLRDNAK ELGNG CFEF YHKCDNECME SVRNGTYDYP QYSEEARLKR EGSSGSSGYI PEAPRDGQAY VRKDGEWVLL STFLGHHHHH HHHHGG SGL NDIFEAQKIE WHE

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Macromolecule #2: Fab 65C6 Heavy Chain

MacromoleculeName: Fab 65C6 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.716766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVQSGAE VKKPGESLRI SCKGFAYSST YFWISWVRQM PGKGLEWMGR IDPTDSYINY SPSFQGHVTI SVDRSISTVY LQWSSLKAS DTAMYYCAYH RRGHFYGSGS AWDWFESWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
EVQLVQSGAE VKKPGESLRI SCKGFAYSST YFWISWVRQM PGKGLEWMGR IDPTDSYINY SPSFQGHVTI SVDRSISTVY LQWSSLKAS DTAMYYCAYH RRGHFYGSGS AWDWFESWGQ GTLVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVESA SCDKTHTCP

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Macromolecule #3: Fab 65C6 Light Chain

MacromoleculeName: Fab 65C6 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.41201 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVLTQSPLT LSVSPGERAT LSCRASQSVS SNLAWYQQMP GQAPRLLIYG ASTRATGIPA RLSGSASGTE FTLTISSLQS EDFAVYYCQ QYNNWPYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVLTQSPLT LSVSPGERAT LSCRASQSVS SNLAWYQQMP GQAPRLLIYG ASTRATGIPA RLSGSASGTE FTLTISSLQS EDFAVYYCQ QYNNWPYTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6ntf

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 206541
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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