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- EMDB-48167: Neuraminidase complexed with mAb 5-16 -

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Basic information

Entry
Database: EMDB / ID: EMD-48167
TitleNeuraminidase complexed with mAb 5-16
Map data
Sample
  • Complex: Neuraminidase IND11 in complex with mAb 5-16
    • Protein or peptide: Neuraminidase
    • Protein or peptide: mAb 5-16 Heavy chain
    • Protein or peptide: mAb 5-16 Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION
KeywordsPolyclonal antibody / Influenza / Neuraminidase / Cryo-EM / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesInfluenza A virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFerguson JA / Raghavan SSR / Ward AB
Funding support1 items
OrganizationGrant numberCountry
Other private
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 5, 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_48167.png

Downloads & links

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Map

FileDownload / File: emd_48167.map.gz / Format: CCP4 / Size: 325 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 440 pix.
= 319. Å		0.73 Å/pix.
x 440 pix.
= 319. Å		0.73 Å/pix.
x 440 pix.
= 319. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.8535714 - 1.3531629
Average (Standard dev.)0.00018851509 (±0.03216719)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 319.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48167_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48167_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 : Neuraminidase IND11 in complex with mAb 5-16

EntireName: Neuraminidase IND11 in complex with mAb 5-16
Components
  • Complex: Neuraminidase IND11 in complex with mAb 5-16
    • Protein or peptide: Neuraminidase
    • Protein or peptide: mAb 5-16 Heavy chain
    • Protein or peptide: mAb 5-16 Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: CALCIUM ION

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Supramolecule #1: Neuraminidase IND11 in complex with mAb 5-16

SupramoleculeName: Neuraminidase IND11 in complex with mAb 5-16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus

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Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Molecular weightTheoretical: 51.847156 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYSMQLASCV TLTLVLLVNS QHHHHHHGSS SSDYSDLQRV KQELLEEVKK ELQKVKEEII EAFVQELRKR GSLVPRGSGG EYRNWSKPQ CNITGFAPFS KDNSIRLSAG GDIWVTREPY VSCDPDKCYQ FALGQGTTLN NGHSNNTVHD RTPYRTLLMN E LGVPFHLG ...String:
MYSMQLASCV TLTLVLLVNS QHHHHHHGSS SSDYSDLQRV KQELLEEVKK ELQKVKEEII EAFVQELRKR GSLVPRGSGG EYRNWSKPQ CNITGFAPFS KDNSIRLSAG GDIWVTREPY VSCDPDKCYQ FALGQGTTLN NGHSNNTVHD RTPYRTLLMN E LGVPFHLG TRQVCMAWSS SSCHDGKAWL HVCITGNDNN ATASFIYNGR LVDSIGSWSK NILRTQESEC VCINGTCTVV MT DGSASGK ADTKILFVEE GKIVHISTLS GSAQHVEECS CYPRFPGVRC VCRDNWKGSN RPIVDINVKN YSIVSSYVCS GLV GDTPRK SDSVSSSYCL DPNNEKGGHG VKGWAFDDGN DVWMGRTINE TLRLGYETFK VIEGWSKANS KLQTNRQVIV EKGD RSGYS GIFSVEGKSC INRCFYVELI RGRKEETKVW WTSNSIVVFC GTSGTYGTGS WPDGADINLM PI

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Macromolecule #2: mAb 5-16 Heavy chain

MacromoleculeName: mAb 5-16 Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.838407 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVKLVESEGG LVQPGSSMKL SCTASGFTFS DDYMAWVRQV AEKGLEWLAK INFDGTSTYY LDSLKSRFII SRDNAKNILY LQMSSLKSE DTATYYCARA GYYYGSSYWY FDVWGTGTTV TVSS

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Macromolecule #3: mAb 5-16 Light chain

MacromoleculeName: mAb 5-16 Light chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.774132 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
NIVMTQSHKF MSTSLGDRVS ITCKASQDVG PAVAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTD FTLTISNVQS EDLADYFCQ QYSSYPLTFG SGTKLEIK

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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: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #6: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm

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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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 117508
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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