9DEZ image
Deposition Date 2024-08-29
Release Date 2024-11-13
Last Version Date 2025-07-30
Entry Detail
PDB ID:
9DEZ
Keywords:
Title:
PDCoV S trimer bound by three copies of PD41 Fab
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spike glycoprotein
Chain IDs:A, B, C
Chain Length:1166
Number of Molecules:3
Biological Source:Porcine deltacoronavirus
Polymer Type:polypeptide(L)
Molecule:PD41 Fab variable heavy-chain
Chain IDs:D (auth: H), E (auth: I), F (auth: J)
Chain Length:118
Number of Molecules:3
Biological Source:Mus musculus
Polymer Type:polypeptide(L)
Molecule:PD41 Fab variable light-chain
Chain IDs:G (auth: L), H (auth: M), I (auth: N)
Chain Length:111
Number of Molecules:3
Biological Source:Mus musculus
Primary Citation
Isolation and escape mapping of broadly neutralizing antibodies against emerging delta-coronaviruses.
Immunity 57 2914 ? (2024)
PMID: 39488210 DOI: 10.1016/j.immuni.2024.10.001

Abstact

Porcine delta-coronavirus (PDCoV) spillovers were recently detected in febrile children, underscoring the recurrent zoonoses of divergent CoVs. To date, no vaccines or specific therapeutics are approved for use in humans against PDCoV. To prepare for possible future PDCoV epidemics, we isolated PDCoV spike (S)-directed monoclonal antibodies (mAbs) from humanized mice and found that two, designated PD33 and PD41, broadly neutralized a panel of PDCoV variants. Cryoelectron microscopy (cryo-EM) structures of PD33 and PD41 in complex with the S receptor-binding domain (RBD) and ectodomain trimer revealed the epitopes recognized by these mAbs, rationalizing their broad inhibitory activity. We show that both mAbs competitively interfere with host aminopeptidase N binding to neutralize PDCoV and used deep-mutational scanning epitope mapping to associate RBD antigenic sites with mAb-mediated neutralization potency. Our results indicate a PD33-PD41 mAb cocktail may heighten the barrier to escape. PD33 and PD41 are candidates for clinical advancement against future PDCoV outbreaks.

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Primary Citation of related structures