8BBN image
Entry Detail
PDB ID:
8BBN
Keywords:
Title:
SARS-CoV-2 Delta-RBD complexed with BA.2-10 and EY6A Fabs
Biological Source:
PDB Version:
Deposition Date:
2022-10-14
Release Date:
2023-03-22
Method Details:
Experimental Method:
Resolution:
3.58 Å
R-Value Free:
0.31
R-Value Work:
0.26
R-Value Observed:
0.26
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:BA.2-10 heavy chain
Chain IDs:I (auth: H), L (auth: C), O (auth: A)
Chain Length:230
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:BA.2-10 light chain
Chain IDs:H (auth: L), K (auth: D), N (auth: B)
Chain Length:214
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:EY6A Heavy chain
Chain IDs:A (auth: M), C (auth: J), E
Chain Length:226
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:EY6A light chain
Chain IDs:B (auth: N), D (auth: K), F
Chain Length:215
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Spike protein S1
Chain IDs:G (auth: R), J (auth: Y), M (auth: X)
Chain Length:202
Number of Molecules:3
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.

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Primary Citation of related structures