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- EMDB-48873: Structure of AG2-G02 Fab in complex with influenza H3N8 A/Mallard... -

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Basic information

Entry
Database: EMDB / ID: EMD-48873
TitleStructure of AG2-G02 Fab in complex with influenza H3N8 A/Mallard/Alberta/362/2017 Hemagglutinin
Map data
Sample
  • Complex: AG2-G02 Fab in complex with influenza H3N8 A/Mallard/Alberta/362/2017 hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Variable domain of the heavy chain of Fab AG2-G02
    • Protein or peptide: Variable domain of the light chain of Fab AG2-G02
  • Protein or peptide: Hemagglutinin
KeywordsInfluenza / Antibody / Immune system / Hemagglutinin / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGopal AB / Wu NC / Lv H / Pholcharee T
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI167910 United States
CitationJournal: To Be Published
Title: Structure of AG2-G02 Fab in complex with influenza H3N8 A/Mallard/Alberta/362/2017 Hemagglutinin
Authors: Gopal AB / Wu NC / Lv H / Pholcharee T
History
DepositionFeb 2, 2025-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48873.png

Downloads & links

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Map

FileDownload / File: emd_48873.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: 0.121
Minimum - Maximum-0.0018049262 - 1.8024011
Average (Standard dev.)0.00066434435 (±0.019412134)
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: #2

Fileemd_48873_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_48873_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 : AG2-G02 Fab in complex with influenza H3N8 A/Mallard/Alberta/362/...

EntireName: AG2-G02 Fab in complex with influenza H3N8 A/Mallard/Alberta/362/2017 hemagglutinin
Components
  • Complex: AG2-G02 Fab in complex with influenza H3N8 A/Mallard/Alberta/362/2017 hemagglutinin
    • Protein or peptide: Hemagglutinin
    • Protein or peptide: Variable domain of the heavy chain of Fab AG2-G02
    • Protein or peptide: Variable domain of the light chain of Fab AG2-G02
  • Protein or peptide: Hemagglutinin

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Supramolecule #1: AG2-G02 Fab in complex with influenza H3N8 A/Mallard/Alberta/362/...

SupramoleculeName: AG2-G02 Fab in complex with influenza H3N8 A/Mallard/Alberta/362/2017 hemagglutinin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Hemagglutinin was expressed recombinantly in SF9 cells. AG2-G02 Fab was expressed recombinantly in Expi293F cells.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 420 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 / Strain: A/Mallard/Alberta/362/2017
Molecular weightTheoretical: 55.422828 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 QEQTSLYVQA 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: Variable domain of the heavy chain of Fab AG2-G02

MacromoleculeName: Variable domain of the heavy chain of Fab AG2-G02 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.807328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVQSGAEM KKPGASVKVS CKASGYTFSA YYIHWVRQAP GQGLEWMGRI NTDSGGTNFA QQFEGRVTMT RDTSISTAYM ELSSLRSDD TAVYYCARGY DFWLGSYRAG GWFDPWGQGT LVTVSS

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Macromolecule #3: Variable domain of the light chain of Fab AG2-G02

MacromoleculeName: Variable domain of the light chain of Fab AG2-G02 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.858151 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPGT LSLSPGERAT LSCRASQSVS SSYLAWYQQK PGQAPRLLIY GASSRATGIP DRFRGSGSGT DFTLTISRLE PEDFAVYYC QQYGSSPQGF TFGPGTKVDI K

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Macromolecule #4: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Mallard/Alberta/362/2017
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl, 100 mM NaCl, 10 mM CaCl2, pH 8.0
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
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 prior to applying to 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: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 326211
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)

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