8DCE image
Deposition Date 2022-06-16
Release Date 2022-06-29
Last Version Date 2024-11-20
Entry Detail
PDB ID:
8DCE
Title:
SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 1 Bound to C144 scFv
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
I 2 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Spike protein S1
Gene (Uniprot):S
Mutations:T333M,A348P,V362Y,A363Y,N394Q,Y396F,I468T,H519D,A522P
Chain IDs:B (auth: A)
Chain Length:210
Number of Molecules:1
Biological Source:Severe acute respiratory syndrome coronavirus 2
Polymer Type:polypeptide(L)
Molecule:C144 scFv
Chain IDs:A (auth: H)
Chain Length:276
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response.
Sci Adv 8 eabq8276 eabq8276 (2022)
PMID: 36103542 DOI: 10.1126/sciadv.abq8276

Abstact

The receptor binding domain (RBD) of the SARS-CoV-2 spike protein is the primary target of neutralizing antibodies and is a component of almost all current vaccines. Here, RBD immunogens were created with stabilizing amino acid changes that improve the neutralizing antibody response, as well as characteristics for production, storage, and distribution. A computational design and in vitro screening platform identified three improved immunogens, each with approximately nine amino acid changes relative to the native RBD sequence, and four key changes conserved between immunogens. The changes are adaptable to all vaccine platforms and compatible with mutations in emerging variants of concern. The immunogens elicit higher levels of neutralizing antibodies than native RBD, focus the immune response to structured neutralizing epitopes, and have increased production yields and thermostability. Incorporating these variant-independent amino acid changes in next-generation COVID vaccines may enhance the neutralizing antibody response and lead to longer duration and broader protection.

Legend

Protein

Chemical

Disease

Primary Citation of related structures