A structural view of coronavirus-receptor interactions

Abstract

In the coronavirus (CoV), the envelope spike (S) glycoprotein is responsible for CoV cell entry and host-to-host transmission. The S is a multifunctional glycoprotein that mediates both attachment of CoV particles to cell surface receptor molecules as well as membrane penetration by fusion. Receptor-binding domains (RBD) have been identified in the S of diverse CoV; they usually contain antigenic determinants targeted by antibodies that neutralize CoV infections. To penetrate host cells, the CoV can use various cell surface molecules, although they preferentially bind to ectoenzymes. Several crystal structures have determined the folding of CoV RBD and the mode by which they recognize cell entry receptors. Here we review the CoV-receptor complex structures reported to date, and highlight the distinct receptor recognition modes, common features, and key determinants of the binding specificity. Structural studies have established the basis for understanding receptor recognition diversity in CoV, its evolution and the adaptation of this virus family to different hosts. CoV responsible for recent outbreaks have extraordinary potential for cross-species transmission; their RBD bear large platforms specialized in recognition of receptors from different species, which facilitates host-to-host circulation and adaptation to man.

Keywords: Coronavirus; Ectoenzymes; Glycoproteins; Virus entry; Virus neutralization; Virus–receptor.

Fig. 1

The CoV S glycoprotein and CoV cell surface receptors. Scheme of a CoV S with the functional domains in the S1 and S2 regions, which are exposed in the virus envelope. The N-terminal signal peptide (SP) and the transmembrane region (TM) are also shown. The N-terminal domain (NTD) that can act as a receptor-binding domain (N-RBD) and the canonical CoV RBD in the C-terminal portion of S1 are indicated. The heptad repeat regions (HR1 and HR2) and the putative fusion peptide (FP) are marked in S2. The arrowhead indicates the putative protease cleavage site in some CoV. Cell entry receptor molecules identified for the indicated CoV (Belouzard et al., 2012) are shown beneath their respective RBD regions. Sialic acids recognized by TGEV and IBV should be considered attachment factors.

Fig. 2

Structures of alpha-CoV RBD and receptor-binding surfaces. (A) Ribbon diagram of the TGEV RBD structure (PDB ID 4F2M) (Reguera et al., 2012). β-Strands (numbered) are shown in light or dark blue, coils in orange, and the helix in red; a β-bulge at β-strand 5 is in magenta. N- and C-terminal ends on the terminal side of the structure are indicated in lowercase letters. The Asn residues at glycosylation sites and the attached glycans defined in the structure are shown as a ball-and-stick model, with carbons in yellow. Cysteine residues and disulphide bonds are shown as green cylinders. The two β-turns at the β-barrel domain tip are labeled. Ribbon diagrams of the PRCV and hCoV-NL63 RBD structures are shown in B and C, respectively. The structures of these domains were determined in complex with the APN (PRCV, PDB ID 4F5C) and ACE2 (NL63, PDB ID 3KBH) (Reguera et al., 2012, Wu et al., 2009). Receptor-binding surfaces in the RBD are shown in pink or red (tyrosine or tryptophan residues) and were generated by the RBD residues that contact the respective receptor molecules in the structures.

Fig. 3

Alpha-CoV recognition of cell entry receptors. Crystal structures of alpha-CoV RBD in complex with the ectodomains of APN (A) and ACE2 (B). (A) Ribbon drawing of the dimeric structure of the PRCV RBD–APN complex (PDB ID 4F5C) (Reguera et al., 2012). Pig APN molecules are shown with domains in orange (N-terminal DI), yellow (DII), red (DIII) and green (C-terminal DIV), as well as the N-terminal ends near the putative location of the cell membrane. The RBD is shown as ribbon and surface drawings in blue and cyan, with the APN-binding tyrosine and tryptophan residues at the RBD tip in red. (B) Ribbon drawing of the hCoV-NL63 RBD–ACE2 complex (PDB ID 3KBH) (Wu et al., 2009). The ACE2 molecule is shown with the two lobes in green (N-terminal) and orange (C-terminal). The RBD is shown as ribbon and surface drawings in blue, with the ACE2-binding residue in pink and the aromatic residues that contact the receptor in red. The N- and C-terminal ends of the receptor molecules are marked in lowercase letters, N-linked glycans are shown as sticks with carbons in yellow, and the zinc ion at the catalytic sites of APN and ACE2 as cyan spheres. For A and B, details of key virus–receptor binding motifs are shown beneath the complex structures. Interaction of the PRCV RBD β1–β2 and β3–β4 turns (shown as sticks) at the domain tip with cavities in the APN (ribbon and surface drawings). The tyrosine at the β1–β2 turn contacts APN residues and the NAG carbohydrate (yellow surface), which is N-linked to pig APN Asn736. The tryptophan side chain at the β3–β4 turn penetrates between DII and DIV. Interaction of the concave center of the hCoV-NL63 RBD tip with the ACE2 β4–β5 turn. Lys535 at the tip of the ACE2 turn is labeled. The ACE2 α-helices α1 and α10 contact the most exposed regions of the RBD loops. Sides chains of buried residues in the virus–receptor interfaces are shown with oxygens in red and nitrogens in blue in this and the following figures; hydrogen bonds are dark dashed lines.

Fig. 4

SARS-CoV RBD and binding to ACE2. (A) Ribbon drawing of the SARS-CoV RBD (PDB ID 2AJF) (Li et al., 2005a), with the core subdomain in yellow and the inserted subdomain in dark red. The β-strands and α-helices are labeled with numbers and uppercase letters, respectively. Terminal ends are labeled in yellow and disulphide bonds in green; Asn residues at glycosylation sites and the attached glycans are shown as sticks, with carbons in yellow. SARS-CoV residues that bind to the ACE2 receptor and define the receptor-binding surface are pink. (B) Ribbon drawing of the SARS-CoV RBD–ACE2 complex (PDB ID 2AJF) (Li et al., 2005a). ACE2 is shown as in Fig. 3B and the RBD as in panel A. The three main ACE2 regions recognized by SARS-CoV are labeled in green. (C) Key virus–receptor binding motifs. ACE2 residues are shown, with carbons in green. In the RBD, receptor-binding tyrosines and an arginine are shown, with carbons in pink, whereas the two critical residues for SARS-CoV adaptation to human ACE2 (Asn479 and Thr487) are shown, with carbons in magenta.

Fig. 5

SARS-CoV neutralizing Ab bind to the RBD. Ribbon drawing of the SARS-CoV RBD in complex with three neutralizing Ab (Hwang et al., 2006, Pak et al., 2009, Prabakaran et al., 2006). The three RBD–Ab crystal structures were superimposed based on the RBD. The RBD is shown as in Fig. 4A and the variable domains of the Ab in green (80R, PDB ID 2GHW), blue (F26G19, PDB ID 3BGF) and cyan (m396, PDB ID 2DD8). RBD Ile489, which is recognized by the m396 and F26G19 Ab (Pak et al., 2009, Prabakaran et al., 2006), is black. Side chains of residues that change in scape mutants to the neutralization are shown in red (Rockx et al., 2010).

Fig. 6

The MERS-CoV RBD and comparison with the SARS RBD. (A) Ribbon drawing of the MERS-CoV RBD (PDB ID 4KRo) (Lu et al., 2013), shown as for SARS-CoV RBD in Fig. 4A, but with the core subdomain in dark yellow. MERS-CoV residues that bind to its DPP4 receptor define the receptor-binding surface (pink). The arrowhead indicates the small “canyon” on one side of the DPP4-binding surface. (B) Stereo view of superimposed MERS- (yellow) and SARS-CoV (red) RBD, core subdomain-based. The β-strands of the MERS-CoV inserted subdomain are labeled and the two conserved in the SARS-CoV are red.

Fig. 7

MERS-CoV RBD binding to DPP4. (A) Ribbon drawing of the dimeric MERS-CoV RBD–DPP4 complex structure (PDB ID 4KRo) (Lu et al., 2013). The DPP4 monomers are shown with the N-terminal β-propeller domain in green and the C-terminal α/β-hydrolase domain in orange. The RBD molecules are as in Fig. 6A. Labels and glycosylation are as in previous figures. (B) Key virus–receptor binding motifs. The virus-binding DPP4 β-propeller blades IV and V are shown in light and dark green, respectively. DPP4 residues are shown, with carbons in green. In the RBD, residues in the small “canyon” that interact with the exposed α-helix in the blade linker are shown, with carbons in magenta, whereas those that bind to the DPP4 N-linked glycan (Asn229) are shown, with carbons pink. Some residues in the two receptor-binding motifs and the external subdomain β-strands (β6 − β9) are labeled.

Fig. 8

Structure of the S glycoprotein NTD. (A) Ribbon drawing of the human galectin-3 carbohydrate recognition domain (CRD) bound to galactose (PDB ID 1A3K) (Seetharaman et al., 1998). The β-strands in the β-barrel are in light or dark blue, and a galactose ligand on the top of the β-sheet is shown as sticks, with carbons in yellow. N- and C-terminal ends are indicated in lowercase letters. (B) Ribbon drawing of the MHV NTD structure (PDB ID 3R4D) (Peng et al., 2011). The β-strands in the central galectin-like β-barrel are in light or dark blue, and those on the top of the sheet are in pink. The Asn residues at glycosylation sites and the attached glycans defined in the structure are shown as sticks, with carbons in yellow. Cysteine residues and disulphide bonds are shown as green sticks.

Fig. 9

MHV recognition of its CEACAM1 receptor. (A) The MHV NTD structure with the CEACAM1-binding surface. The NTD ribbon diagram is shown as in Fig. 8B. The surface of the N-terminal MHV residues that form a socket is shown in violet and that of the other receptor-binding residues is pink. MHV Leu160 in the bottom of the socket is shown in red. (B) The MHV NTD in complex with the CEACAM1 receptor (PDB ID 3R4D) (Peng et al., 2011). The CEACAM1 N-terminal D1 is shown in green, with the β-strands in the receptor-binding CFG β-sheet labeled. The side chain of CEACAM1 Ile41 that penetrates the NTD socket is shown as spheres. The MHV Leu160 in the socket and Leu174 that contacts the top of D1 are in red. (C) Key virus–receptor binding motifs. Side chains of some receptor-binding MHV residues are shown, with carbons in pink; the hydrophobic residues in the bottom of the socket and Leu174 are in magenta; the CEACAM1 residues are in green. Ile41 in the CC′ loop, the most important virus-binding motif in CEACAM-1 (Peng et al., 2011), is shown as spheres.

Fig. 10

Structural view of the multifunctional CoV S binding to host cell surface receptors. The two domains, NTD and RBD, of the S1 region that CoV use for attachment to cell surface molecules (Fig. 1) docked into the cryo-electron microscopy map (gray) of the trimeric SARS-CoV S (EMD-1423) (Beniac et al., 2006). Ribbon representations of the SARS-CoV RBD (yellow) and the MHV NTD (blue) alone or bound to ACE2 (Fig. 4B) and to CEACAM1 D1 (Fig. 9B), respectively.