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- EMDB-48118: Map of Neuraminidase active site specific polycloncal antibody fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-48118
TitleMap of Neuraminidase active site specific polycloncal antibody from sera of 10 mice vaccinated with Indiana 2011 Group 2 Neuraminidase
Map data
Sample
  • Complex: A/Indiana/10/2011 Neuraminidase in complex with polyclonal antobodies
    • Protein or peptide: A/Indiana/10/2011 Group 2 Neruaminidase Tetramer
KeywordsNeuraminidase / Antibody / Influenza / Mouse / Polyclonal / VIRAL PROTEIN
Biological speciesInfluenza A virus (A/Indiana/10/2011(H3N2))
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsFerguson JA / Han J / Rodriguez AJ / Torres JL / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Sci Adv / Year: 2025
Title: Functional and epitope specific monoclonal antibody discovery directly from immune sera using cryo-EM.
Authors: James A Ferguson / Sai Sundar Rajan Raghavan / Garazi Peña Alzua / Disha Bhavsar / Jiachen Huang / Alesandra J Rodriguez / Jonathan L Torres / Maria Bottermann / Julianna Han / Florian ...Authors: James A Ferguson / Sai Sundar Rajan Raghavan / Garazi Peña Alzua / Disha Bhavsar / Jiachen Huang / Alesandra J Rodriguez / Jonathan L Torres / Maria Bottermann / Julianna Han / Florian Krammer / Facundo D Batista / Andrew B Ward /
Abstract: Antibodies are crucial therapeutics, comprising a substantial portion of approved drugs due to their safety and clinical efficacy. Traditional antibody discovery methods are labor-intensive, limiting ...Antibodies are crucial therapeutics, comprising a substantial portion of approved drugs due to their safety and clinical efficacy. Traditional antibody discovery methods are labor-intensive, limiting scalability and high-throughput analysis. Here, we improved upon our streamlined approach combining structural analysis and bioinformatics to infer heavy and light chain sequences from cryo-EM (cryo-electron microscopy) maps of serum-derived polyclonal antibodies (pAbs) bound to antigens. Using ModelAngelo, an automated structure-building tool, we accelerated pAb sequence determination and identified sequence matches in B cell repertoires via ModelAngelo-derived hidden Markov models (HMMs) associated with pAb structures. Benchmarking against results from a nonhuman primate HIV vaccine trial, our pipeline reduced analysis time from weeks to under a day with higher precision. Validation with murine immune sera from influenza vaccination revealed multiple protective antibodies. This workflow enhances antibody discovery, enabling faster, more accurate mapping of polyclonal responses with broad applications in vaccine development and therapeutic antibody discovery.
History
DepositionDec 2, 2024-
Header (metadata) releaseAug 27, 2025-
Map releaseAug 27, 2025-
UpdateAug 27, 2025-
Current statusAug 27, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48118.png

Downloads & links

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Map

FileDownload / File: emd_48118.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 371.2 Å		0.73 Å/pix.
x 512 pix.
= 371.2 Å		0.73 Å/pix.
x 512 pix.
= 371.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.35876128 - 0.5916162
Average (Standard dev.)-0.000036414087 (±0.015166852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 371.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48118_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_48118_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : A/Indiana/10/2011 Neuraminidase in complex with polyclonal antobodies

EntireName: A/Indiana/10/2011 Neuraminidase in complex with polyclonal antobodies
Components
  • Complex: A/Indiana/10/2011 Neuraminidase in complex with polyclonal antobodies
    • Protein or peptide: A/Indiana/10/2011 Group 2 Neruaminidase Tetramer

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Supramolecule #1: A/Indiana/10/2011 Neuraminidase in complex with polyclonal antobodies

SupramoleculeName: A/Indiana/10/2011 Neuraminidase in complex with polyclonal antobodies
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Macromolecule #1: A/Indiana/10/2011 Group 2 Neruaminidase Tetramer

MacromoleculeName: A/Indiana/10/2011 Group 2 Neruaminidase Tetramer / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza A virus (A/Indiana/10/2011(H3N2))
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYSMQLASCV TLTLVLLVNS QHHHHHHGSS SSDYSDLQRV KQELLEEVKK ELQKVKEEII EAFVQELRKR GSLVPRGSGG EYRNWSKPQC NITGFAPFSK DNSIRLSAGG DIWVTREPYV SCDPDKCYQF ALGQGTTLNN GHSNNTVHDR TPYRTLLMNE LGVPFHLGTR ...String:
MYSMQLASCV TLTLVLLVNS QHHHHHHGSS SSDYSDLQRV KQELLEEVKK ELQKVKEEII EAFVQELRKR GSLVPRGSGG EYRNWSKPQC NITGFAPFSK DNSIRLSAGG DIWVTREPYV SCDPDKCYQF ALGQGTTLNN GHSNNTVHDR TPYRTLLMNE LGVPFHLGTR QVCMAWSSSS CHDGKAWLHV CITGNDNNAT ASFIYNGRLV DSIGSWSKNI LRTQESECVC INGTCTVVMT DGSASGKADT KILFVEEGKI VHISTLSGSA QHVEECSCYP RFPGVRCVCR DNWKGSNRPI VDINVKNYSI VSSYVCSGLV GDTPRKSDSV SSSYCLDPNN EKGGHGVKGW AFDDGNDVWM GRTINETLRL GYETFKVIEG WSKANSKLQT NRQVIVEKGD RSGYSGIFSV EGKSCINRCF YVELIRGRKE ETKVWWTSNS IVVFCGTSGT YGTGSWPDGA DINLMPI

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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

Concentration0.5 mg/mL
BufferpH: 7.4 / Details: Tris-Buffered Saline
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 25 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 3 / Number real images: 15368 / Average electron dose: 43.4 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.8 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 190000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 436610
CTF correctionSoftware - Name: cryoSPARC (ver. v4.3.0) / Software - details: PatchCTF / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 72780
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.3.0)
Final 3D classificationNumber classes: 1 / Avg.num./class: 72780 / Software - Name: cryoSPARC (ver. v4.3.0)

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