dcyphr | Structural basis of a shared antibody response to SARS-CoV-2



Understanding how antibodies to SARS-CoV-2 work on the molecular level could help with vaccine and drug development. In this study, the researchers analyzed 294 anti-SARS-CoV-2 antibodies. They found that a gene called IGHV-53 is the most frequent gene that is targeted by the receptor-binding domain of the SARS-CoV-2 spike protein, which is a major surface protein the virus uses to bind to human cell receptors and allows infection to begin. The researchers crystallized the structure of the antibodies that target IGHV-53 with the RBD. These IGHV3-53 antibodies show high affinity for SARS-CoV-2 RBD, which is promising for vaccine design. Understanding binding structure and mechanisms could help facilitate designing antigens to neutralize SARS-CoV-2 antibodies for vaccine and drug development.


The ongoing COVID-19 pandemic urgently requires the development of an effective vaccine. Currently, there are multiple candidates but the mechanism by which these candidates contribute to an effective antibody response is unclear on the molecular level. Shared antibody responses, in which the same genetic elements and mechanisms of antigen recognition, have been observed for many infectious diseases. Characterizing antibody interactions with microbial antigens can provide insight into the immune response against these diseases and ideas about vaccine design against them.

The spike (S) protein is the most important SARS-CoV-2 surface protein for human infection. The S protein uses a receptor-binding domain (RBD) which binds to the human surface receptor ACE2, so that the virus can enter a human cell and begin infection. Antibodies that target this RBD would be effective by preventing SARS-CoV-2 from entering human cells. A number of these antibodies have been discovered, which the researchers compiled into a list and found that IGHV3-53 is the most frequently used immunoglobulin heavy chain variable (IGHV) gene by these antibodies. IGHV genes encode the heavy chain of antibodies, which have a variable portion that differs between different microbes that are targeted. IGHV3-53 antibodies had lower mutation rates and were more potent, making them a promising candidate for vaccine design.

The researchers determined crystal structures of two IGHV3-53 neutralizing antibodies encoded by IGHV-53, CC12.1 and CC12.3, when bound to SARS-CoV-2 RBD. Both CC12.1 and CC12.3 had few mutations when they adapted to effectively bind SARS-CoV-2. They also had high binding affinities with SARS-CoV-2 RBD. In addition, previous studies suggested that CC12.1 and CC12.3 bind to a similar epitope (where antibodies attach to antigens) in ACE2, but not similar to CR3022. CR3022 is another antibody that also binds the SARS-CoV-2 RBD. If CC12.1, CC12.3, and CR3022 all targeted the same epitope, they would be in competition with one another.

The researchers determined four complex crystal structures, CC12.1/RBD, CC12.3/RBD, CC12.1/RBD/CR3022, and CC12.3/RBD/CR3022 at different resolutions. They found that CC12.1 and CC12.3 bind to SARS-CoV-2 RBD in an identical manner. Among 17 ACE2 binding locations in the SARS-CoV-2 RBD, 15 are epitopes of CC12.1 and 11 are epitopes of CC12.3.

The researchers analyzed the molecular interactions between the RBD and CC12.1 and CC12.3 to understand why IGHV3-53 is used as a shared antibody response. The two antibodies interacted with the RBD through specific hydrogen bonds. None of these interactions mimic ACE2 binding to SARS-CoV-2 RBD.

The researchers found two key patterns in the IGHV3-53 gene that are important for binding: an NY motif at residues 32 and 33, and an SGGS motif at residues 53 to 56. The NY motif hydrogen bonds with a carbonyl group on the RBD, which enhances and stabilizes binding. The SGSS motif forms a hydrogen bond network with the RBD that also strengthens binding.

The NY and SGSS motifs are both encoded in the IGHV3-53 gene. Overall, the researchers identified two motifs that enable IGHV3-53 to target SARS-CoV-2 RBD. Although the binding mechanism of the two motifs are highly similar, a region of the antibodies called CDR H3 interacts with the RBD differently between the two antibodies, which is due to differences in CDR H3 genetic sequences and conformations. This demonstrates that IGHV3-53 can produce versatile and varying ways to target ACE2 in SARS-CoV-2 RBD. In addition, the CDR H3 of these two antibodies are interesting in that their sequences are shorter than other human antibodies. This is a unique molecular feature of the IGHV3-53-encoded response to SARS-CoV-2, but there are other antibodies in this gene that need further investigation of their binding mechanisms.

Other IGHV-encoded antibodies are frequently observed in the immune response against SARS-CoV-2, and need further characterization. The characterization of IGHV3-53 antibodies as described in this study are a promising starting point for vaccine design, with little affinity maturation and highly potent neutralization capabilities. As IGHV3-53 is frequently found in healthy people, this antibody response could be successfully and easily evoked with a vaccine.