9K6J image
Deposition Date 2024-10-22
Release Date 2026-01-07
Last Version Date 2026-01-07
Entry Detail
PDB ID:
9K6J
Title:
Crystal structure of SARS-CoV-2 WT RBD bound with P5-1C8 Fab
Biological Source:
Expression System(s):
Method Details:
Experimental Method:
Resolution:
2.39 Å
R-Value Free:
0.28
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:H chain of P5-1C8 Fab
Chain IDs:B (auth: A)
Chain Length:217
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:L chain of P5-1C8 Fab
Chain IDs:C (auth: B)
Chain Length:211
Number of Molecules:1
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:A (auth: C)
Chain Length:271
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2
Ligand Molecules
Primary Citation
IgG-Bridging-Seeded Synergistic Aggregation of SARS-CoV-2 Spikes Underlies Potent Neutralization by a Low-Affinity Antibody.
Adv Sci ? e17192 e17192 (2025)
PMID: 41355083 DOI: 10.1002/advs.202517192

Abstact

Mechanistic studies of viral neutralization typically prioritize high-affinity antibodies, relegating low-affinity binders to the sidelines. P5‑1C8, a Class 1 SARS-CoV-2 antibody that exemplifies this underexplored "low‑affinity yet high‑potency" phenotype is reported, retaining strong neutralization of Omicron JN.1 despite markedly weakened trimer binding (KD = 225 nM; IC50 = 0.06 nM). Structural and biophysical analyses reveal that P5-1C8 engages WT and BA.1 spikes through canonical intra-spike bivalency, but with JN.1 it induces aggregation. Using virion-like nanoparticles displaying multiple spikes, it is shown that IgG remains bound with no detectable dissociation and triggers pronounced aggregation. Coarse-grained molecular dynamics delineate the stepwise pathway in which weak IgG-spike contacts seed aggregation via transient inter-spike bridging. Together, these findings establish the first mechanistic framework demonstrating how weak-binding antibodies can nonetheless achieve potent neutralization through higher-order aggregation, thereby expanding the conceptual landscape of antibody function and opening new directions for antibody evaluation and design.

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Primary Citation of related structures
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