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- EMDB-46727: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/20... -

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Basic information

Entry
Database: EMDB / ID: EMD-46727
TitleStructure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
Map data
Sample
  • Complex: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: Heavy chain of influenza virus hemagglutinin antibody AG11-2F01
    • Protein or peptide: Light chain of influenza virus hemagglutinin antibody AG11-2F01
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantibody-antigen complex / 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 speciesInfluenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMou Z / Lei R / Dai X / Wu N
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI167910 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)DP2 AT011966 United States
Michelson Medical Research FoundationPrize for Human Immunology and Vaccine Research United States
Searle Scholars Program United States
CitationJournal: Sci Transl Med / Year: 2025
Title: High-throughput synthesis and specificity characterization of natively paired influenza hemagglutinin antibodies with oPool display.
Authors: Wenhao O Ouyang / Huibin Lv / Wenkan Liu / Ruipeng Lei / Zongjun Mou / Tossapol Pholcharee / Logan Talmage / Meixuan Tong / Wei Ji / Yiquan Wang / Katrine E Dailey / Akshita B Gopal / Danbi ...Authors: Wenhao O Ouyang / Huibin Lv / Wenkan Liu / Ruipeng Lei / Zongjun Mou / Tossapol Pholcharee / Logan Talmage / Meixuan Tong / Wei Ji / Yiquan Wang / Katrine E Dailey / Akshita B Gopal / Danbi Choi / Madison R Ardagh / Lucia A Rodriguez / Jenna J Guthmiller / Xinghong Dai / Nicholas C Wu /
Abstract: Antibody discovery is crucial for developing therapeutics and vaccines and for understanding adaptive immunity. However, the lack of approaches to synthesize antibodies with defined sequences in a ...Antibody discovery is crucial for developing therapeutics and vaccines and for understanding adaptive immunity. However, the lack of approaches to synthesize antibodies with defined sequences in a high-throughput manner represents a major bottleneck in antibody discovery. Here, we present oPool display, a high-throughput cell-free platform that combined oligo pool synthesis and mRNA display to rapidly construct and characterize hundreds to thousands of natively paired antibodies in parallel. As a proof of concept, we applied oPool display to probe the binding specificity of more than 300 uncommon influenza hemagglutinin-specific antibodies against nine hemagglutinin variants through 16 screens. More than 5000 binding tests were performed in 3 to 5 days of hands-on time with further scaling potential. Follow-up structural and functional analysis of two antibodies revealed the versatility of the human immunoglobulin gene segment D3-3 () in recognizing the hemagglutinin stem. Overall, this study established an experimental platform that not only accelerates antibody characterization but also enables unbiased discovery of recurring molecular signatures among antibodies with the same specificity.
History
DepositionAug 23, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46727.png

Downloads & links

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Map

FileDownload / File: emd_46727.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.)
0.66 Å/pix.
x 512 pix.
= 337.92 Å		0.66 Å/pix.
x 512 pix.
= 337.92 Å		0.66 Å/pix.
x 512 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.1856133 - 1.8306562
Average (Standard dev.)-0.00008917441 (±0.05557885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 337.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_46727_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_46727_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 : Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/20...

EntireName: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
Components
  • Complex: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: Heavy chain of influenza virus hemagglutinin antibody AG11-2F01
    • Protein or peptide: Light chain of influenza virus hemagglutinin antibody AG11-2F01
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/20...

SupramoleculeName: Structure of AG11-2F01 Fab in complex with A/Solomon Islands/3/2006 (H1N1) influenza virus hemagglutinin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1)

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Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1)
Molecular weightTheoretical: 35.809098 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLGIAPLQ LGNCSVAGWI LGNPECELLI SRESWSYIVE KPNPENGTC YPGHFADYEE LREQLSSVSS FERFEIFPKE SSWPNHTTTG VSASCSHNGE SSFYKNLLWL TGKNGLYPNL S KSYANNKE ...String:
DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLGIAPLQ LGNCSVAGWI LGNPECELLI SRESWSYIVE KPNPENGTC YPGHFADYEE LREQLSSVSS FERFEIFPKE SSWPNHTTTG VSASCSHNGE SSFYKNLLWL TGKNGLYPNL S KSYANNKE KEVLVLWGVH HPPNIGDQRA LYHKENAYVS VVSSHYSRKF TPEIAKRPKV RDQEGRINYY WTLLEPGDTI IF EANGNLI APRYAFALSR GFGSGIINSN APMDECDAKC QTPQGAINSS LPFQNVHPVT IGECPKYVRS AKLRMVTGLR NIP S

UniProtKB: Hemagglutinin

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Macromolecule #2: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus / Strain: A/Solomon Islands/3/2006(H1N1)
Molecular weightTheoretical: 19.395527 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
IAGFIEGGWT GMVDGWYGYH HQNEQGSGYA ADQKSTQNAI NGITNKVNSV IEKMNTQFTA VGKEFNKLER RMENLNKKVD DGFIDIWTY NAELLVLLEN ERTLDFHDSN VKNLYEKVKS QLKNNAKEIG NGCFEFYHKC NDECMESVKN GTYDYPKYSE E SKLNREKI

UniProtKB: Hemagglutinin

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Macromolecule #3: Heavy chain of influenza virus hemagglutinin antibody AG11-2F01

MacromoleculeName: Heavy chain of influenza virus hemagglutinin antibody AG11-2F01
type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.794432 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCAVSGNSIS SEYYWAWIRQ PPGMPPEWVG TIYHTGNTYY NPSLKSRTTI SMDTSKNQFS LRLRSVTAA DSAVYYCARA GVTIFGLTLP NYFHHWGQGT LVTVSS

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Macromolecule #4: Light chain of influenza virus hemagglutinin antibody AG11-2F01

MacromoleculeName: Light chain of influenza virus hemagglutinin antibody AG11-2F01
type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.486814 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IQMTQSPSTL SASVGDRVTI TCRASQSISN WMAWYQQKPG KAPKLLIYKA STLESGVPSR FSGGGSGPEF TLTISSLQPD DSATYYCQQ YNSYMYTFGQ GTKVEI

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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: 6 / 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: 8
Component:
ConcentrationNameFormula
20.0 mMTris Hydrochloric acid
100.0 mMSodium ChlorideNaCl
10.0 mMCalcium ChlorideCaCl2

Details: 20 mM Tris-HCl, 100 mM NaCl, 10 mM CaCl2, pH 8.0
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 359720
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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