8ZC2 image
Entry Detail
PDB ID:
8ZC2
EMDB ID:
Title:
SARS-CoV-2 Omicron BA.2 spike trimer (6P) in complex with D1F6 Fab, head-to-head aggregate
Biological Source:
PDB Version:
Deposition Date:
2024-04-28
Release Date:
2024-05-29
Method Details:
Experimental Method:
Resolution:
7.82 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Spike glycoprotein
Mutations:681-684del, F817P, A892P, A899P, A942P, K986P, V987P
Chain IDs:A, B, C, J (auth: D), K (auth: E), L (auth: F)
Chain Length:1240
Number of Molecules:6
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Description:Light chain of D1F6 Fab
Chain IDs:D (auth: G), F (auth: M), G (auth: N), M (auth: I), O (auth: K), P (auth: L)
Chain Length:223
Number of Molecules:6
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Heavy chain of D1F6 Fab
Chain IDs:E (auth: H), H (auth: Q), I (auth: R), N (auth: J), Q (auth: O), R (auth: P)
Chain Length:230
Number of Molecules:6
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
An unconventional VH1-2 antibody tolerates escape mutations and shows an antigenic hotspot on SARS-CoV-2 spike.
Cell Rep 43 114265 114265 (2024)
PMID: 38805396 DOI: 10.1016/j.celrep.2024.114265

Abstact

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein continues to evolve antigenically, impacting antibody immunity. D1F6, an affinity-matured non-stereotypic VH1-2 antibody isolated from a patient infected with the SARS-CoV-2 ancestral strain, effectively neutralizes most Omicron variants tested, including XBB.1.5. We identify that D1F6 in the immunoglobulin G (IgG) form is able to overcome the effect of most Omicron mutations through its avidity-enhanced multivalent S-trimer binding. Cryo-electron microscopy (cryo-EM) and biochemical analyses show that three simultaneous epitope mutations are generally needed to substantially disrupt the multivalent S-trimer binding by D1F6 IgG. Antigenic mutations at spike positions 346, 444, and 445, which appeared in the latest variants, have little effect on D1F6 binding individually. However, these mutations are able to act synergistically with earlier Omicron mutations to impair neutralization by affecting the interaction between D1F6 IgG and the S-trimer. These results provide insight into the mechanism by which accumulated antigenic mutations facilitate evasion of affinity-matured antibodies.

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Primary Citation of related structures