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- EMDB-45930: Structure of 16.ND.92 Fab in complex with A/Solomon Islands/3/200... -

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Basic information

Entry
Database: EMDB / ID: EMD-45930
TitleStructure of 16.ND.92 Fab in complex with A/Solomon Islands/3/2006(H1N1) influenza virus Hemagglutinin
Map data
Sample
  • Complex: 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hemagglutinin
    • Protein or peptide: Variable Heavy Chain of 16.ND.92 Fab
    • Protein or peptide: Variable Light Chain of 16.ND.92 Fab
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2
KeywordsAntibody / Influenza / 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 (A/Solomon Islands/3/2006(H1N1))
Methodsingle particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsOuyang WO / Pholcharee T / Wu NC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)DP2 AT011966 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
DepositionJul 25, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45930.png

Downloads & links

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Map

FileDownload / File: emd_45930.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: 0.089
Minimum - Maximum-0.0018061608 - 1.8738102
Average (Standard dev.)0.00070432463 (±0.01964024)
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_45930_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_45930_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 : 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hema...

EntireName: 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hemagglutinin
Components
  • Complex: 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hemagglutinin
    • Protein or peptide: Variable Heavy Chain of 16.ND.92 Fab
    • Protein or peptide: Variable Light Chain of 16.ND.92 Fab
    • Protein or peptide: Hemagglutinin HA1
    • Protein or peptide: Hemagglutinin HA2

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Supramolecule #1: 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hema...

SupramoleculeName: 16.ND.92 Fab in complex with A/Solomon Islands/3/2006 (H1N1) Hemagglutinin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Both Hemagglutinin and Fab were recombinantly expressed and purified. The Fab was then mixed with Hemagglutinin at 3.5:1 ratio. The complex were then isolated using size exclusion chromatography.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Variable Heavy Chain of 16.ND.92 Fab

MacromoleculeName: Variable Heavy Chain of 16.ND.92 Fab / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.659272 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVESGGGL VQPGGSLRLS CEASGFTLSS YWMHWVRQDP GKGLVWVAVI NSDGSSTDYA DFVKGRFTIS RDNAKNTVYL QMNSLRAED TAVYYCARAP QGTVFGVVII GADGFDIWGQ GTMVTVSS

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Macromolecule #2: Variable Light Chain of 16.ND.92 Fab

MacromoleculeName: Variable Light Chain of 16.ND.92 Fab / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.800195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IQMTHIPVSL SASVGDRVTI TCRASQSISS WLAWYQQKPG KAPKLLIYKA STLESGVPSR FSGSGSGTDF TLTINSLQPD DFATYYCQH YNTYSRAWTF GQGTKVEV

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Macromolecule #3: Hemagglutinin HA1

MacromoleculeName: Hemagglutinin HA1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Molecular weightTheoretical: 35.851199 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLKGIAPL QLGNCSVAGW ILGNPECELL ISRESWSYIV EKPNPENGT CYPGHFADYE ELREQLSSVS SFERFEIFPK ESSWPNHTTT GVSASCSHNG ESSFYKNLLW LTGKNGLYPN L SKSYANNK ...String:
DTICIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDSHNGK LCRLKGIAPL QLGNCSVAGW ILGNPECELL ISRESWSYIV EKPNPENGT CYPGHFADYE ELREQLSSVS SFERFEIFPK ESSWPNHTTT GVSASCSHNG ESSFYKNLLW LTGKNGLYPN L SKSYANNK EKEVLVLWGV HHPPNIGDQR ALYHKENAYV SVVSSHYSRK FTPEIAKRPK VRDQEGRINY YWTLLEPGDT II FEANGNL IAPRYAFALS RGFGSGIINS NAPMDECDAK CQTPQGAINS SLPFQNVHPV TIGECPKYVR SAKLRMVTGL RNI P

UniProtKB: Hemagglutinin

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Macromolecule #4: Hemagglutinin HA2

MacromoleculeName: Hemagglutinin HA2 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Molecular weightTheoretical: 19.412537 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
LFGAIAGFIE GGWTGMVDGW YGYHHQNEQG SGYAADQKST QNAINGITNK VNSVIEKMNT QFTAVGKEFN KLERRMENLN KKVDDGFID IWTYNAELLV LLENERTLDF HDSNVKNLYE KVKSQLKNNA KEIGNGCFEF YHKCNDECME SVKNGTYDYP K YSEESKLN R

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

Concentration3 mg/mL
BufferpH: 7.5 / Details: 20mM Tris-HCl, 150mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Blot force: 0, Blot time: 3 s, Humidity 90%, and 4 C..

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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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 152449
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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