Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 (Spike_S1_RBD_SARS-CoV-2)
Type: Domain

The CoV Spike (S) protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesised as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). Most CoVs, including SARS-CoV-2, SARS-CoV, and MERS-CoV use the C-domain to bind their receptors. However, CoV such as mouse hepatitis virus (MHV) uses the NTD to bind its receptor, mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a). The S1 NTD contributes to the Spike trimer interface .

This entry represents the RBD domain of Spike protein S1 subunit from SARS-CoV-2, which binds the extracellular peptidase domain of angiotensin-converting enzyme 2 (ACE2). It has been shown that the receptor binding induces the dissociation of the S1 with ACE2, prompting the S2 to transit from a metastable pre-fusion to a more-stable post-fusion state that is essential for membrane fusion . Recent structures revealed that only a single RBD is necessary for ACE2 binding and it is not yet clear if protrusion of the RBD from the S protein trimer is necessary for binding to ACE2 or the interconversion of the RBD between closed and open states represents an intrinsic property of the S protein . During the pandemic, many amino acid substitutions have been reported in the S1 segment, being D614G the most commonly observed amino acid change from the reference sequence. Although it was estimated to be slightly destabilizing, it was hypothesized that it increases virus infectivity by increasing the total amount of S protein incorporated into virions. The most prevalent RBD substitution in the RBD is the T478I, located in a portion of a loop that contacts ACE2. However, most substitutions in the interface with ACE2 appear to be neutral or destabilizing, with none improving binding affinity .

SARS-CoV-2 RBD has a core formed by a twisted five-stranded antiparallel β-sheet (β1-7) with short helices and loops connecting them. Between the β4 and β7 strands in the core, there is an extended insertion, the receptor-binding motif (RBM), containing the short β5 and β6 strands, α4 and α5 helices and loops, which contains most of the contacting residues for binding to ACE2. There are nine cysteine residues in the RBD, eight of which form four pairs of disulfide bonds. Among these four pairs, three are in the core which help to stabilise the β-sheet structure, while the remaining pair connects the loops in the distal end of the RBM .