The spike (S) protein of CoVs mediates binding and fusion events necessary for infection and is the major target of protective immunity [
2,
4,
23,
24]. Although the S protein of SARS-CoV shares little amino acid identity (approximately 20%–27%), it shares common structural features with S proteins of other CoVs [
2,
25]. SARS-CoV S protein is a type 1 transmembrane glycoprotein of approximately 1255 amino acids in length and divided into two functional domains S1 (amino acids 15–680) and S2 (amino acids 681–1255) () [
2,
25–
27]. In many CoVs the S protein is cleaved during biogenesis and these two functional domains are held together non-covalently; however, like hCoV 229E, the S protein is not cleaved in SARS-CoV [
2,
25].
The S1 domain forms a globular structure that mediates interaction of the S protein with its receptor, angiotensin-converting enzyme 2 (ACE2) [
25,
27,
28]. A region of S1 consisting of 193 amino acids (amino acids 318–510) is the minimal receptor binding domain (RBD) () [
29]. Five cysteine residues within the RBD are important for efficient expression of the RBD and formation of the RBD structure [
27]. There are three functional glycosylation sites within the RBD located at amino acids 318, 330, and 357. Expression of S protein requires glycosylation of at least one site; however, glycosylation does not affect ACE2 binding [
30].
Co-crystallization of the RBD and human ACE2 identified a concave surface consisting of 70 amino acids (424–494), which contacts the tip of ACE2 and is defined as the receptor binding motif (RBM) () [
27]. Basic residues found between amino acids 422 to 463 appeared to be important for mediating entry of S pseudotyped virus [
31]. The alteration of either of the two basic residues, R441A and R453A within this domain, abolished pseudovirus entry [
31]. However, the effect of the R441A mutation may be due to decreased protein expression [
30]. Interestingly, none of the eight basic residues within the RBM, including R441 and R453, were altered in 96 clinical isolates () [
31]. Two residues, R426 and N473, were identified as critical for ACE2 binding [
30]. Changes in the RBM, namely N479K and T487S (), might have allowed more efficient binding to human ACE2 [
3,
17,
27,
32].
The S2 domain mediates fusion and contains the putative fusion peptide and two conserved helical regions (HR1 and HR2) which upon cleavage by the endosomal protease cathepsin L form the six helix bundle fusion core () [
2,
25,
33–
37]. These two regions are connected by a long (170 amino acid) inter-domain loop likely allowing flexibility to facilitate fusion [
25]. The HR1 domain forms the inner helical coiled coil region onto which the HR2 domain associates in an anti-parallel manner to form the fusion core [
25,
34,
35,
37]. This brings the putative fusion peptide (770–788) in close proximity to the transmembrane domain and facilitates juxtaposition of the cellular and viral membranes required for fusion [
37,
38]. Therapies that disrupt interactions of the HR1 and HR2 domains would likely confer protection, and synthetic HR2 peptides have been demonstrated to block SARS-CoV infection, however HR1 peptides have not been found to inhibit entry [
37]. Abs targeted to S2 can disrupt viral entry (discussed below).
The cellular glycoprotein CD209L (L-SIGN), also found on type II pneumocytes, has been described as an alternate receptor or a co-receptor for SARS-CoV [
39]. Infectivity mediated by L-SIGN, albeit at a significantly lower efficiency than ACE2, has been demonstrated in non-permissive cells [
39,
40]. Residues important for S interaction with L-SIGN vary from the defined RBD, with several residues mapping N-terminal to the RBD. Neutralizing Abs that interrupt the association of S and ACE2 fail to prevent L-SIGN mediated entry [
40]. The interaction of S protein with dendritic cell-specific ICAM-3 grabbing non-integrin (DC-SIGN) can facilitate the entry of SARS-CoV via ACE2. This interaction domain of S protein is between amino acids 324 and 386 within the minimum RBD, but N-terminal to the RBM [
41]. DC-SIGN has also been implicated in the ability of dendritic cells (DCs) to transfer SARS-CoV to target cells
in vitro without productively infecting the DCs, similar to HIV [
42].