8CBD image
Deposition Date 2023-01-25
Release Date 2024-02-07
Last Version Date 2024-11-20
Entry Detail
PDB ID:
8CBD
Keywords:
Title:
SARS-CoV-2 Delta-RBD complexed with BA.4/5-1 and EY6A Fabs
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.52 Å
R-Value Free:
0.26
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:EY6A heavy chain
Chain IDs:D (auth: E), F (auth: G), H (auth: J)
Chain Length:226
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:EY6A light chain
Chain IDs:E (auth: F), G (auth: I), I (auth: K)
Chain Length:215
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:BA.4/5-1 heavy chain
Chain IDs:B (auth: H), K (auth: A), N (auth: C)
Chain Length:222
Number of Molecules:3
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:BA.4/5-1 light chain
Chain IDs:C (auth: L), L (auth: B), O (auth: D)
Chain Length:214
Number of Molecules:3
Biological Source:Homo sapiens
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:A (auth: R), J (auth: X), M (auth: Y)
Chain Length:202
Number of Molecules:3
Biological Source:Severe acute respiratory syndrome coronavirus 2
Ligand Molecules
Primary Citation
Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection.
Nat Commun 15 3284 3284 (2024)
PMID: 38627386 DOI: 10.1038/s41467-024-47393-3

Abstact

The rapid evolution of SARS-CoV-2 is driven in part by a need to evade the antibody response in the face of high levels of immunity. Here, we isolate spike (S) binding monoclonal antibodies (mAbs) from vaccinees who suffered vaccine break-through infections with Omicron sub lineages BA.4 or BA.5. Twenty eight potent antibodies are isolated and characterised functionally, and in some cases structurally. Since the emergence of BA.4/5, SARS-CoV-2 has continued to accrue mutations in the S protein, to understand this we characterize neutralization of a large panel of variants and demonstrate a steady attrition of neutralization by the panel of BA.4/5 mAbs culminating in total loss of function with recent XBB.1.5.70 variants containing the so-called 'FLip' mutations at positions 455 and 456. Interestingly, activity of some mAbs is regained on the recently reported variant BA.2.86.

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Primary Citation of related structures