8C3V image
Deposition Date 2022-12-28
Release Date 2023-03-22
Last Version Date 2024-11-13
Entry Detail
PDB ID:
8C3V
Keywords:
Title:
SARS-CoV-2 Delta-RBD complexed with BA.2-13 Fab and C1 nanobody
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.74 Å
R-Value Free:
0.25
R-Value Work:
0.21
R-Value Observed:
0.21
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:BA.2-13 heavy chain
Chain IDs:A (auth: H), I (auth: A), K (auth: C)
Chain Length:231
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Nanobody C1
Chain IDs:D (auth: I), F (auth: J), H (auth: K)
Chain Length:131
Number of Molecules:3
Biological Source:Lama glama
Polymer Type:polypeptide(L)
Molecule:BA.2-13 light chain
Chain IDs:B (auth: L), J (auth: B), L (auth: D)
Chain Length:213
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:C (auth: R), E (auth: X), G (auth: Y)
Chain Length:202
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus 2
Primary Citation

Abstact

In November 2021, Omicron BA.1, containing a raft of new spike mutations, emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 and then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional receptor-binding domain (RBD) amino acid substitutions compared with BA.2. We describe a panel of 25 potent monoclonal antibodies (mAbs) generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titer of vaccine or BA.1, BA.2, or BA.4/5 immune serum.

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Primary Citation of related structures