Human coronavirus spike protein-host receptor recognition

Abstract

A variety of coronaviruses (CoVs) have infected humans and caused mild to severe respiratory diseases that could result in mortality. The human CoVs (HCoVs) belong to the genera of α- and β-CoVs that originate in rodents and bats and are transmitted to humans via zoonotic contacts. The binding of viral spike proteins to the host cell receptors is essential for mediating fusion of viral and host cell membranes to cause infection. The SARS-CoV-2 originated in bats (RaTG13 SARS-CoV) and is transmitted to humans via pangolins. The presence of 'PRRA' sequence motif in SARS-CoV-2 spike proteins from human, dog, cat, mink, tiger and lion suggests a common viral entry mechanism into host cells. In this review, we discuss structural features of HCoV spike proteins and recognition of host protein and carbohydrate receptors.

Keywords: Amino peptidase N; Angiotensin-converting enzyme 2; Dipeptidyl peptidase 4; HCoV-229E; HCoV-HKU1; HCoV-NL63; HCoV-OC43; Human coronavirus; MERS-CoV; Receptor binding domain; SARS-CoV; SARS-CoV-2; Sialic acid; Spike protein.

Fig. 1A

Phylogenetic tree of representative spike proteins from human coronaviruses. SARS-CoV, SARS-CoV-2, MERS-CoV, HCoV-HKU1, HCoV-NL63, NCoV-229E and HCoV-OC43.

Fig. 1B

Amino acid sequence and structural annotation of human SARS-CoV-2 spike protein (NCBI code: QHD43416). The N-glycosylation sites are shown in bold and italics. Structural regions are labelled below the sequence.

Fig. 1C

Human SARS-CoV-2 spike protein (PDB code:6VSBA-chain). S1^A domain (27–300, green), S1^A-S1^B linker (301–335, pink), S1^B domain (336–516, purple), 517–533 (linker, golden rod), S1^C domain (534–589, orange), 590–593 (linker, golden rod), S1^D domain (594–674, cyan), protease cleavage site (675–688, blue), S1–S2 subunits linker (689–710, orange), central β-strand (711–737, magenta), downward helix (738–782, red), S2′ cleavage site (783–815, sea green), fusion peptide (816–833, navy blue), connecting region (834–910, yellow), heptad repeats (912–983, chartreuse), central helix (984–1034, dodger blue), β-hairpin (1035–1069, brown), connecting β-sheet domain (1070–1134, spring green).

Fig. 1D

Structural superposition of apo SARS-CoV (PDB code:6ACC) and human ACE-2 receptor complexes (6ACG, 6ACJ, 6ACK). The pre-fusion to post-fusion conformations are indicated. 6ACC: brown (S1^B downward), 6ACG: conformation 1, spike (blue), ACE-2 (dodger blue), 6ACJ: conformation 2, spike (red), ACE-2 (orange), 6ACK: conformation 3, spike (green), ACE-2 (chartreuse).

Fig. 2A

Cartoon representation of SARS-CoV spike protein S1^Bdomain (PDB code:3SCI) (green) interacting with human ACE-2 (purple). Strand β4 (orange), strand β5 (cyan), extended loop (pink) and the side chains of residues within 4.5 Å from ACE-2 (K390, R426, Y436, Y440, F442, L443, P462, D463, F472, N473, Y475, N479, Y481, G482, Y484, T486, T487, G488, I489, Y491) are indicated. The disulfide bridge C467–C474 (yellow). The residues involved in the hydrogen bonds with ACE-2 are shown in bold and italics.

Fig. 2B

Cartoon representation of the SARS-CoV-2 spike protein S1^Bdomain (green) interacting with human ACE-2 (purple) (PDB code:6LZG). Strand β4 (orange) and β5 (cyan), the extended loop (pink) and the side chains of residues within 4.5 Å from ACE-2 (K417, G446, Y449, Y453, L455, F456, Y473, A475, G476, E484, F486, N487, Y489, F490, Q493, G496, Q498, T500, N501, G502, Y505) are indicated within 4.5 Å from ACE-2. The disulfide bridge C480–C488 (yellow). The residues that form hydrogen bonds with ACE-2 are shown in bold and italics.

Fig. 2C

Phylogenetic tree of SARS-CoV and SARS-CoV-2 spike proteins. Human SARS-CoV-2 (light green), dog SARS-CoV-2 (black), cat SARS-CoV-2 (aqua green), mink SARS-CoV-2 (magenta), tiger SARS-CoV-2 (orange), lion SARS-CoV-2 (yellow), pangolin SARS-CoV (cyan), human SARS-CoV (dark green), bat SARS-CoV (red), civet SARS-CoV (violet).

Fig. 2D

Portion of the alignment of spike proteins. Extracted from the multiple sequence alignment (Supplementary Fig. S2) showing the insertion sequences that form receptor binding motifs within the RBD (S1^B domain) for human SARS-CoV-2 (1–3), Canis lupus familiaris SARS-CoV-2 (4), Felis catus SARS-CoV-2 (5), Mustela lutreola SARS-CoV-2 (6), Neovison vison SARS-CoV-2 (7), Panthera tigris SARS-CoV-2 (8), Panthera leo SARS-CoV-2 (9), bat SARS-CoV RaTG13 (10), pangolin SARS-CoV (11), bat SARS-CoV (12–17), civet SARS-CoV (18–19), human SARS-CoV (20–21). The secondary structure conformations; β-strands (olive green arrows) and α-helices (red bars) are indicated. The starting and ending amino acid numbers of the regions are indicated after the NCBI code within brackets.

Fig. 3A

Cartoon representation of the MERS-CoV spike protein (PDB code:6Q04) S1^Adomain binding to O-sialic acid. The side chains of residues (Q36, F39, H91, A92, F101, I132, S133, P134, S135, Q304, R307) that lie within 4.5 Å from sialic acid are indicated. The residues that form hydrogen bonds with O-sialic acid are shown in bold and italics.

Fig. 3B

Cartoon representation of the MERS-CoV spike protein (PDB code:4L72) S1^Bdomain (green) interacting with human DPP4 (purple). The strand β4 (orange) and β5 (cyan), the extended loop (pink) and the side chains of residues within 4.5 Å from DPP4 (S454, D455, P463, Y499, N501, K502, S504, L506, D510, R511, E513, P515, E536, D537, G538, D539, Y540, R542, W553, V555, A556, S557, S559) are indicated. The C503–C526 disulfide bridge (yellow). The residues that form hydrogen bonds with DPP4 are shown in bold and italics.

Fig. 4A

Cartoon representation of the HCoV-OC43 spike protein (PDB code:6NZK) S1^Adomain binding to O-sialic acid. The side chains of residues within 4.5 Å from sialic acid (N27, K29, T31, L80, K81, G82, S83, L85, L86, S87, W90) are indicated. The residues that form hydrogen bonds with sialic acid are shown in bold and italics.

Fig. 4B

Cartoon representation of the HCoV-OC43 spike protein (PDB code:6NZK) S1^Bdomain (green). The strands β4 (orange) and β5 (cyan) and the extended loop (pink) are indicated. The Cys-Cys pairs; 591–597, 491–561, 535–548, 571–578, 535–548, 499–522, 501–576 form disulfide bridges (yellow).

Fig. 4C

Cartoon representation of the HCoV-HKU1 spike protein (PDB code:5KWB) S1^Bdomain (green). The strands β4 (orange) and β5 (cyan) and the extended loop (pink) are indicated. The Cys-Cys pairs; 466–546, 474–495, 476–567, 520–533, 504–518, 485–516, 582–588, 556–569 form disulfide bridges (yellow).

Fig. 4D

Cartoon representation of the HCoV-NL63 spike protein (PDB code:3KBH) S1^Bdomain (green) interacting with human ACE-2. The three loops (gold, blue, magenta) connecting the strands β1 (orange) to β2 (green), β3 (cyan) to β4 (green) and β5 (red) to β6 (green), along with side chains of residues lie with 4.5 Å from hACE-2 (G494, G495, S496, C497, Y498, V499, C500, H503, G534, S535, P536, G537, S539, S540, W585, H586) are shown. The C497–C500 forms disulfide bridge (yellow). The residues that form hydrogen bonds with ACE-2 are shown in bold and italics.

Fig. 4E

Cartoon representation of the HCoV-229E spike protein (PDB code:6ATK) S1^Bdomain (green) interacting with human APN. The three loops (gold, blue, magenta) connecting strands β1 (orange) to β2 (green), β3 (cyan) to β4 (green) and β5 (red) to β6 (green), respectively, along with side chains of residues that lie within 4.5 Å from hAPN (S312, G313, G314, G315, K316, C317, F318, N319, C320, R359, W404, S407, K408) are shown. The C317–C320 forms disulfide bridge (yellow). The residues that form hydrogen bonds with APN are shown in bold and italics.