8ERR image
Deposition Date 2022-10-12
Release Date 2022-10-26
Last Version Date 2024-11-06
Entry Detail
PDB ID:
8ERR
Title:
SARS-CoV-2 Omicron BA.1 spike ectodomain trimer in complex with the S2X324 neutralizing antibody Fab fragment
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Spike glycoprotein
Gene (Uniprot):S
Chain IDs:A, B, C
Chain Length:1274
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Molecule:S2X324 heavy chain
Chain IDs:D (auth: H), F (auth: E), H (auth: I)
Chain Length:119
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:S2X324 light chain
Chain IDs:E (auth: L), G (auth: F), I (auth: J)
Chain Length:110
Number of Molecules:3
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation

Abstact

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages carry distinct spike mutations resulting in escape from antibodies induced by previous infection or vaccination. We show that hybrid immunity or vaccine boosters elicit plasma-neutralizing antibodies against Omicron BA.1, BA.2, BA.2.12.1, and BA.4/5, and that breakthrough infections, but not vaccination alone, induce neutralizing antibodies in the nasal mucosa. Consistent with immunological imprinting, most antibodies derived from memory B cells or plasma cells of Omicron breakthrough cases cross-react with the Wuhan-Hu-1, BA.1, BA.2, and BA.4/5 receptor-binding domains, whereas Omicron primary infections elicit B cells of narrow specificity up to 6 months after infection. Although most clinical antibodies have reduced neutralization of Omicron, we identified an ultrapotent pan-variant-neutralizing antibody that is a strong candidate for clinical development.

Legend

Protein

Chemical

Disease

Primary Citation of related structures