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- EMDB-48607: Structure of porcine Fab 14-1 in complex with influenza H1N1 A/So... -

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Basic information

Entry
Database: EMDB / ID: EMD-48607
TitleStructure of porcine Fab 14-1 in complex with influenza H1N1 A/Solomon Island/3/2006 hemagglutinin
Map data
Sample
  • Complex: A complex of hemagglutinin from A A/Hawaii/70/2019 with pig Fab 24-1G17
    • Protein or peptide: Hemagglutinin (HA1 polypeptide) from influenza H1N1 A/Solomon Island/3/2006
    • Protein or peptide: Hemagglutinin (HA2 polypeptide) from influenza H1N1 A/Solomon Island/3/2006
  • Protein or peptide: Heavy chain of Fab from porcine antibody 14-1
  • Protein or peptide: Light chain of Fab from porcine antibody 14-1
KeywordsInfluenza / Hemagglutinin / Antibody / Immune response / Pig / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


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 / 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: 2.61 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_48607.png

Downloads & links

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Map

FileDownload / File: emd_48607.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 720 pix.
= 380.88 Å		0.53 Å/pix.
x 720 pix.
= 380.88 Å		0.53 Å/pix.
x 720 pix.
= 380.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.529 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.047
Minimum - Maximum-0.0018430024 - 1.8138463
Average (Standard dev.)0.00069834874 (±0.019785177)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 380.87997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48607_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_48607_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 : 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 (HA1 polypeptide) from influenza H1N1 A/Solomon Island/3/2006
    • Protein or peptide: Hemagglutinin (HA2 polypeptide) from influenza H1N1 A/Solomon Island/3/2006
  • Protein or peptide: Heavy chain of Fab from porcine antibody 14-1
  • Protein or peptide: Light chain of Fab from porcine antibody 14-1

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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: #1-#2
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 (HA1 polypeptide) from influenza H1N1 A/Solomon Isl...

MacromoleculeName: Hemagglutinin (HA1 polypeptide) from influenza H1N1 A/Solomon Island/3/2006
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 36.450879 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: ADTICIGYHA NNSTDTVDTV LEKNVTVTHS VNLLEDSHNG KLCLLKGIAP LQLGNCSVAG WILGNPECEL LISRESWSYI VEKPNPENG TCYPGHFADY EELREQLSSV SSFERFEIFP KESSWPNHTT TGVSASCSHN GESSFYKNLL WLTGKNGLYP N LSKSYANN ...String:
ADTICIGYHA NNSTDTVDTV LEKNVTVTHS VNLLEDSHNG KLCLLKGIAP LQLGNCSVAG WILGNPECEL LISRESWSYI VEKPNPENG TCYPGHFADY EELREQLSSV SSFERFEIFP KESSWPNHTT TGVSASCSHN GESSFYKNLL WLTGKNGLYP N LSKSYANN KEKEVLVLWG VHHPPNIGDQ RALYHKENAY VSVVSSHYSR KFTPEIAKRP KVRDQEGRIN YYWTLLEPGD TI IFEANGN LIAPRYAFAL SRGFGSGIIN SNAPMDECDA KCQTPQGAIN SSLPFQNVHP VTIGECPKYV RSAKLRMVTG LRN IPSIQS R

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin (HA2 polypeptide) from influenza H1N1 A/Solomon Isl...

MacromoleculeName: Hemagglutinin (HA2 polypeptide) from influenza H1N1 A/Solomon Island/3/2006
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 25.066264 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFI DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNDECM ESVKNGTYDY P KYSEESKL ...String:
GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINGITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFI DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNDECM ESVKNGTYDY P KYSEESKL NREKIDGVKL ESMGVYQILA IYSTVASSLV LLVSLGAISF WMCSNGSLQC RICI

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Macromolecule #3: Heavy chain of Fab from porcine antibody 14-1

MacromoleculeName: Heavy chain of Fab from porcine antibody 14-1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.673274 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EEKLVESGGG LVQPGGSLRL GCVGSGFTFS SAYINWVRQA PGKGLEWLAA IRTSGGGTYY ADSVKGRFTI SRDDSQNTAY LQMNSLRTE DTARYYCAAG AMTMVVASFF QYYAMDLWGP GVEVVVSS

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Macromolecule #4: Light chain of Fab from porcine antibody 14-1

MacromoleculeName: Light chain of Fab from porcine antibody 14-1 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 11.737934 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QTVIQEPAMS VSPGGTVTLT CAFSSGSVTS GDYPSWFQQT PGQPPRLLIY RTNNRPTGVP SRFSGAISGN KAALTITGAQ ANDEADYYC TLYTSSLNNI FGGGTHLTVL GQP

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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: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 363401
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)

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