Part:BBa_K4040019

CR3022 scFv Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
COMPATIBLE WITH RFC[21]
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 352
Illegal NgoMIV site found at 688
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI.rc site found at 568

Usage and Biology

CR3022 is a SARS-CoV neutralizing antibody to a highly conserved epitope on the receptor-binding domain (RBD) on the spike protein that is able to cross-react with SARS-CoV-2. A single-chain variable fragment (scFv) is not actually a fragment of an antibody, but instead is a fusion protein of the variable regions of the heavy (VH) and light chains (VL) of immunoglobulins, connected with a short linker peptide of ten to about 25 amino acids. The linker is usually rich in glycine for flexibility, as well as serine or threonine for solubility, and can either connect the N-terminus of the VH with the C-terminus of the VL or vice versa. This protein retains the specificity of the original immunoglobulin, despite the removal of the constant regions and the introduction of the linker. These molecules were created to facilitate phage display, where it is highly convenient to express the antigen-binding domain as a single peptide. As an alternative, scFv can be created directly from subcloned heavy and light chains derived from a hybridoma. ScFvs have many uses, e.g., flow cytometry, immunohistochemistry, and as antigen-binding domains of artificial T cell receptors (chimeric antigen receptor). CR3022 scFv is an scFv protein derived from the antibody CR3022.

Experimental results

A Broad-spectrum neutralizing antibody

CR3022 was previously isolated from a SARS survivor and neutralizes SARS-CoV [1], CR3022 was recently found to also be a cross-reactive antibody that can bind to both SARS-CoV-2 and SARS-CoV [19]. Our recent crystal structure demonstrated that CR3022 targets a highly conserved cryptic epitope on the receptor binding domain (RBD) of the S protein [20]. The CR3022 epitope is exposed only when the RBD is in the “up” but not the “down” conformation on the S protein [20]. A few SARS-CoV-2 antibodies from COVID-19 patients have also recently been shown to target the CR3022 epitope [12,17,21], suggesting that it is an important site of vulnerability for the antibody response in SARS-CoV-2 infection. Out of 28 residues in the CR3022 epitope, 24 are conserved between SARS-CoV-2 and SARS-CoV, explaining the cross-reactive binding of CR3022. However, CR3022 has a higher affinity to SARS-CoV than to SARS-CoV-2 (>100-fold difference), and can neutralize SARS-CoV, but not SARS-CoV-2, in a live virus neutralization assay [20]. Therefore, CR3022 provides a good case study to probe antigenic variation between SARS-CoV-2 and SARS-CoV and the effects on antibody cross-neutralization.

Figure 1: Crystal structure of SARS-CoV receptor binding domain in complex with human antibody CR3022. The structure has been resolved [1] available in PDB with accession number 7JN5.

Binding to RBD on the spike protein

Used for a CAR

References

Ordered List