Structure of Severe Acute Respiratory Syndrome Coronavirus Receptor-binding Domain Complexed with Neutralizing Antibody

Abstract

The severe acute respiratory syndrome coronavirus (SARSCoV, or SCV), which caused a world-wide epidemic in 2002 and 2003, binds to a receptor, angiotensin-converting enzyme 2 (ACE2), through the receptor-binding domain (RBD) of its envelope (spike, S) glycoprotein. The RBD is very immunogenic; it is a major SCV neutralization determinant and can elicit potent neutralizing antibodies capable of out-competing ACE2. However, the structural basis of RBD immunogenicity, RBD-mediated neutralization, and the role of RBD in entry steps following its binding to ACE2 have not been elucidated. By mimicking immune responses with the use of RBD as an antigen to screen a large human antibody library derived from healthy volunteers, we identified a novel potent cross-reactive SCV-neutralizing monoclonal antibody, m396, which competes with ACE2 for binding to RBD, and determined the crystal structure of the RBD-antibody complex at 2.3-Å resolution. The antibody-bound RBD structure is completely defined, revealing two previously unresolved segments (residues 376 -381 and 503-512) and a new disulfide bond (between residues 378 and 511). Interestingly, the overall structure of the m396-bound RBD is not significantly different from that of the ACE2-bound RBD. The antibody epitope is dominated by a 10-residue-long protruding ␤6 -␤7 loop with two putative ACE2-binding hotspot residues (Ile-489 and Tyr-491). These results provide a structural rationale for the function of a major determinant of SCV immunogenicity and neutralization, the development of SCV therapeutics based on the antibody paratope and epitope, and a retrovaccinology approach for the design of anti-SCV vaccines. The available structural information indicates that the SCV entry may not be mediated by ACE2-induced conformational changes in the RBD but may involve other conformational changes or/and yet to be identified coreceptors.The severe acute respiratory syndrome coronavirus (SARS-CoV, or SCV) 4 infected more than 8000 humans with a fatality rate of ϳ10% (1-4). Although there have been no recent outbreaks, the need to develop potent therapeutics and vaccines against a re-emerging SCV or a related virus remains of high priority. The amazingly rapid pace of SARS research for the last few years has resulted in a wealth of information for the virus, especially about its interactions with the host leading to disease and immune responses, which could also be helpful for the development of strategies to cope with other viral pathogens including influenza and HIV.Entry of viruses into animal cells is initiated by binding to cell-surface-associated receptors and can be prevented by neutralizing antibodies (nAbs) targeting the virus receptor-binding site (5, 6). In the case of SCV entry, the spike (S) glycoprotein (7, 8) binds to a receptor, angiotensin-converting enzyme 2 (ACE2) (9), through the receptor-binding site of its receptor-binding domain (RBD) (7, 10, 11). The RBD is an attractive target for neutralizing antibodies that could prevent SCV entry by blocking the a...

Potent cross-reactive neutralization of SARS coronavirus isolates by human monoclonal antibodies

“…7B), as predicted from the crystal structure of the complex. IgG1 was more potent than Fab, in agreement with its higher effective affinity (avidity) to the surface-associated RBD as measured previously by surface plasmon resonance methodology (36). IgG1 S230.15 also competed with ACE2 for binding to the RBD although at somewhat higher concentration (SI Fig.…”

“…We have recently identified an hmAb, m396, which binds with high affinity to the RBD, and we determined the crystal structure of the RBD⅐m396 complex at high resolution (36). A crystal structure analysis suggested that this antibody could also neutralize the 2003/2004 outbreak isolate GD03.…”

Chicken Heat Shock Protein 90 Is a Component of the Putative Cellular Receptor Complex of Infectious Bursal Disease Virus

“…This is first time that a neutralizing MAb, i.e., MAbSVP-4, was generated using SVP as an antigen. This result further suggests that SVP carries the neutralizing epitopes that could be viral receptor-binding domains, as indicated by studies of other viruses (12,34). Taken together, we suspect that SVP, as IBDV, is able to interact with cellular receptors.…”

Norovirus GII.4 Strain Antigenic Variation

“…Fine-mapping studies with peptides or mutant capsids will be necessary to map key interaction residues. Further, cocrystalization of blocking MAbs with the panel of VLPs may provide structural information important for predicting modes of carbohydrate blockade and mapping epitopes onto the structure (52,60). We have shown here by comparing blockade of GII.4-2002 with GII.…”