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TitleFunctional and epitope specific monoclonal antibody discovery directly from immune sera using cryo-EM.
Journal, issue, pagesSci Adv, Vol. 11, Issue 33, Page eadv8257, Year 2025
Publish dateAug 15, 2025
AuthorsJames 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 /
PubMed AbstractAntibodies 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.
External linksSci Adv / PubMed:40815640 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.4 Å
Structure data

EMDB-48118: Map of Neuraminidase active site specific polycloncal antibody from sera of 10 mice vaccinated with Indiana 2011 Group 2 Neuraminidase
Method: EM (single particle) / Resolution: 3.3 Å

48165

9md2

EMDB-48165, PDB-9md2:
Neuraminidase in complex with mAb 5-6
Method: EM (single particle) / Resolution: 3.4 Å

48166

9md3

EMDB-48166, PDB-9md3:
Neuraminidase in complex with mAb 5-12
Method: EM (single particle) / Resolution: 2.9 Å

48167

9md4

EMDB-48167, PDB-9md4:
Neuraminidase complexed with mAb 5-16
Method: EM (single particle) / Resolution: 2.7 Å

48168

9md5

EMDB-48168, PDB-9md5:
Neuraminidase in complex with mAb 6-23.2
Method: EM (single particle) / Resolution: 2.9 Å

48169

9md6

EMDB-48169, PDB-9md6:
Neuraminidase in complex with mAb 6-23.1
Method: EM (single particle) / Resolution: 2.7 Å

Chemicals

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

ChemComp-CA:
Unknown entry

Source
  • Influenza A virus (A/Indiana/10/2011(H3N2))
  • influenza a virus
  • mus musculus (house mouse)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Polyclonal antibodies / Neuraminidase. Influenza / Cryo-EM / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex / Neuraminidase / Influenza / Polyclonal antibody

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