8BBO image
Deposition Date 2022-10-14
Release Date 2023-03-22
Last Version Date 2024-10-16
Entry Detail
PDB ID:
8BBO
Keywords:
Title:
SARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.75 Å
R-Value Free:
0.25
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 41
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:IGH@ protein
Gene (Uniprot):IGH@
Chain IDs:B (auth: H)
Chain Length:224
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Immunoglobulin kappa light chain
Chain IDs:C (auth: L)
Chain Length:213
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Spike glycoprotein
Gene (Uniprot):S
Chain IDs:A (auth: R)
Chain Length:202
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2
Ligand Molecules
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.

Legend

Protein

Chemical

Disease

Primary Citation of related structures