7XSB image
Deposition Date 2022-05-13
Release Date 2023-05-10
Last Version Date 2024-10-30
Entry Detail
PDB ID:
7XSB
Title:
Crystal structure of SARS-CoV-2 spike receptor binding domain bound with P5S-3B11 Fab
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.20 Å
R-Value Free:
0.32
R-Value Work:
0.25
R-Value Observed:
0.26
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Chain IDs:A (auth: E), B (auth: A), C (auth: B), D (auth: C)
Chain Length:243
Number of Molecules:4
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Molecule:P5S-3B11 Heavy chain
Chain IDs:E (auth: H), G (auth: D), I (auth: G), K (auth: J)
Chain Length:217
Number of Molecules:4
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:P5S-3B11 Light chain
Chain IDs:F (auth: L), H (auth: F), J (auth: I), L (auth: K)
Chain Length:216
Number of Molecules:4
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Infection with wild-type SARS-CoV-2 elicits broadly neutralizing and protective antibodies against omicron subvariants.
Nat.Immunol. 24 690 699 (2023)
PMID: 36914890 DOI: 10.1038/s41590-023-01449-6

Abstact

The omicron variants of SARS-CoV-2 have substantial ability to escape infection- and vaccine-elicited antibody immunity. Here, we investigated the extent of such escape in nine convalescent patients infected with the wild-type SARS-CoV-2 during the first wave of the pandemic. Among the total of 476 monoclonal antibodies (mAbs) isolated from peripheral memory B cells, we identified seven mAbs with broad neutralizing activity to all variants tested, including various omicron subvariants. Biochemical and structural analysis indicated the majority of these mAbs bound to the receptor-binding domain, mimicked the receptor ACE2 and were able to accommodate or inadvertently improve recognition of omicron substitutions. Passive delivery of representative antibodies protected K18-hACE2 mice from infection with omicron and beta SARS-CoV-2. A deeper understanding of how the memory B cells that produce these antibodies could be selectively boosted or recalled can augment antibody immunity against SARS-CoV-2 variants.

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Primary Citation of related structures