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- EMDB-48610: Structure of porcine Fab 15-1 in complex with influenza H3N8 A/Ma... -

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Basic information

Entry
Database: EMDB / ID: EMD-48610
TitleStructure of porcine Fab 15-1 in complex with influenza H3N8 A/Mallard/Alberta/362/2017 hemagglutinin
Map data
Sample
  • Complex: A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 24-1G17
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Heavy chain of Fab from porcine antibody 15-1
    • Protein or peptide: Light chain of Fab from porcine antibody 15-1
KeywordsInfluenza / Hemagglutinin / Antibody / Immune response / Pig / 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 / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsLv H / Pholcharee T / Wu NC
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Emerging Pathogens Initiative United States
CitationJournal: To Be Published
Title: Structural analysis of broadly neutralizing porcine antibodies to influenza hemagglutinin stem
Authors: Lv H / Pholcharee T / Wu NC
History
DepositionJan 11, 2025-
Header (metadata) releaseSep 24, 2025-
Map releaseSep 24, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48610.png

Downloads & links

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Map

FileDownload / File: emd_48610.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 288 pix.
= 304.704 Å		1.06 Å/pix.
x 288 pix.
= 304.704 Å		1.06 Å/pix.
x 288 pix.
= 304.704 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.069
Minimum - Maximum-0.0017917717 - 1.8570073
Average (Standard dev.)0.0016218331 (±0.027325429)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 304.70398 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48610_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_48610_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 2...

EntireName: A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 24-1G17
Components
  • Complex: A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 24-1G17
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Heavy chain of Fab from porcine antibody 15-1
    • Protein or peptide: Light chain of Fab from porcine antibody 15-1

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Supramolecule #1: A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 2...

SupramoleculeName: A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 24-1G17
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Hemagglutinin was expressed recombinantly in SF9 cells. Fab 24-1G17 was expressed recombinantly in Expi293F cells.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 76.19 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: 55.449852 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ATLCLGHHAV PNGTIVKTIT DDQIEVTNAT ELVQSSSTGK ICNNPHRILD GRDCTLIDAL LGDPHCDVFQ DETWDLYVER SSAFSNCYP YDVPDYASLR SLVASSGTLE FITEGFTWTG VTQNGGSNAC KRGPASGFFS RLNWLTKSGS AYPVLNVTMP N NDNFDKLY ...String:
ATLCLGHHAV PNGTIVKTIT DDQIEVTNAT ELVQSSSTGK ICNNPHRILD GRDCTLIDAL LGDPHCDVFQ DETWDLYVER SSAFSNCYP YDVPDYASLR SLVASSGTLE FITEGFTWTG VTQNGGSNAC KRGPASGFFS RLNWLTKSGS AYPVLNVTMP N NDNFDKLY VWGVHHPSTN QEQTNLYVQA SGRVTVSTRR SQQTIIPNIG SRPWVRGQSG RISIYWTIVK PGDVLVINSN GN LIAPRGY FKMRTGKSSI MRSDAPIDTC ISECITPNGS IPNDKPFQNV NKITYGACPK YVKQSTLKLA TGMRNVPEKQ TRG LFGAKA GFIENGWEGM IDGWYGFRHQ NSEGTGQAAD LKSTQAAIDQ INGKLNRVIE KTNEKFHQIE KEFSEVEGRI QDLE KYVED TKIDLWSYNA ELLVALENQH TIDLTDSEMN KLFEKTRRQL RENAEDMGNG CFKIYHKCDN ACIESIRNGT YDHDI YRDE ALNNRFQIKG V

UniProtKB: Hemagglutinin

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Macromolecule #2: Heavy chain of Fab from porcine antibody 15-1

MacromoleculeName: Heavy chain of Fab from porcine antibody 15-1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 12.846277 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EEKLVESGGG LVQPGGSLRL SCVGSGFDLS DYAFSWVRQA PRKGLEWLAA IDSVSYRRST YYADSVKGRF TISSDYSQNT LYLQMNSLR TEDTARYYCA RGAFPNLWGP GVEVVVS

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Macromolecule #3: Light chain of Fab from porcine antibody 15-1

MacromoleculeName: Light chain of Fab from porcine antibody 15-1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 12.073504 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AIVLTQTPLS LSVSPGEPAS ISCRSSQSLR HTDGKDYLNW YLQKPGQSPQ LLIYYATTRA SGVPDRFTGS GSGTDFTLKI SRVEAEDVG VYYCFQGLQS PPGFGAGTKL ELK

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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

Concentration3 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl, 100 mM NaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III
DetailsThe sample was also mixed with octyl glucoside to 0.1% w/v of the detergent final concentration piror to applying on the grid.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Details: Initial model was built directly into the map using automated model building algorithm ModelAngelo (DOI: 10.1038/s41586-024-07215-4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 151566
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)

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