8BCZ image
Deposition Date 2022-10-17
Release Date 2023-03-22
Last Version Date 2025-07-02
Entry Detail
PDB ID:
8BCZ
Keywords:
Title:
SARS-CoV-2 Delta-RBD complexed with Fabs BA.2-36, BA.2-23, EY6A and COVOX-45
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:BA.2-36 heavy chain
Chain IDs:H (auth: A)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:BA.2-36 light chain
Chain IDs:I (auth: B)
Chain Length:106
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:COVOX-45 heavy chain
Chain IDs:D (auth: C)
Chain Length:226
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:COVOX-45 light chain
Chain IDs:E (auth: D)
Chain Length:107
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:EY6A heavy chain
Chain IDs:F (auth: E)
Chain Length:121
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:EY6A light chain
Chain IDs:G (auth: F)
Chain Length:108
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:BA.2-23 heavy chain
Chain IDs:B (auth: H)
Chain Length:119
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:BA.2-23 light chain
Chain IDs:C (auth: L)
Chain Length:107
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Spike protein S1
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.

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Disease

Primary Citation of related structures