Structural insights into immune recognition of the severe acute respiratory syndrome coronavirus S protein receptor binding domain

Abstract

The spike (S) protein of the severe acute respiratory syndrome coronavirus (SARS-CoV) is responsible for host cell attachment and fusion of the viral and host cell membranes. Within S the receptor binding domain (RBD) mediates the interaction with angiotensin-converting enzyme 2 (ACE2), the SARS-CoV host cell receptor. Both S and the RBD are highly immunogenic and both have been found to elicit neutralizing antibodies. Reported here is the X-ray crystal structure of the RBD in complex with the Fab of a neutralizing mouse monoclonal antibody, F26G19, elicited by immunization with chemically inactivated SARS-CoV. The RBD-F26G19 Fab complex represents the first example of the structural characterization of an antibody elicited by an immune response to SARS-CoV or any fragment of it. The structure reveals that the RBD surface recognized by F26G19 overlaps significantly with the surface recognized by ACE2 and, as such, suggests that F26G19 likely neutralizes SARS-CoV by blocking the virus-host cell interaction.

Fig. 1

Stereo ribbon representation of the F26G19 Fab–RBD binding interface. The RBD (in yellow) is shown in complex with the V_H (in blue) and V_L (in red) regions of the F26G19 Fab with the interface between the RBD and the Fab highlighted (in green). Residues 486–492 of the RBD are labeled and the CDRs of the Fab are labeled as H1, H2, H3, L1, L2, and L3. For simplicity, the C_L and C_H regions have been omitted from the figure.

Fig. 2

Stereo diagram of the F26G19 Fab binding site for RBD residues 486–492. RBD residues 486–492 and 494 (green carbon atoms), as well as the F26G19 V_L (pink atoms) and V_H (blue atoms) residues that interact with the 486–492 loop are depicted in stick representation. The molecular surface of F26G19 Fab in the vicinity of the 486–492 loop is depicted (in grey). Intermolecular hydrogen bonds between RBD residues 486–492 and the F26G19 Fab are shown as yellow dashes.

Fig. 3

Molecular surface representation of the F26G19 Fab and ACE2 binding sites on the RBD. The RBD surfaces buried by the F26G19 Fab (in light blue) and ACE2 (in turquoise) overlap at RBD residues 486–491 (in dark blue). The two N-linked glycosylation sites on the RBD (Asn330, Asn357) are illustrated (in red).

Fig. 4

Ribbon representation of the F26G19 Fab–RBD complex and the m396 Fab–RBD, 80R scFv–RBD and ACE2–RBD complexes. The heavy chain and light chain of each neutralizing antibody fragment is depicted in blue and red, respectively, the RBD is depicted in yellow and the ACE2 molecule is depicted in purple. Residues 486–492 of the RBD, which represent the major determinant of F26G19 binding, are depicted in green.