Structural Basis for Human Receptor Recognition by SARS-CoV-2 Omicron Variant BA.1

Abstract

The highly contagious and fast-spreading omicron variant of SARS-CoV-2 infects the respiratory tracts efficiently. The receptor-binding domain (RBD) of the omicron spike protein recognizes human angiotensin-converting enzyme 2 (ACE2) as its receptor and plays a critical role in the tissue tropism of SARS-CoV-2. Here, we showed that the omicron RBD (strain BA.1) binds to ACE2 more strongly than does the prototypic RBD from the original Wuhan strain. We also measured how individual omicron mutations affect ACE2 binding. We further determined the crystal structure of the omicron RBD (engineered to facilitate crystallization) complexed with ACE2 at 2.6 Å. The structure shows that omicron mutations caused significant structural rearrangements of two mutational hot spots at the RBD/ACE2 interface, elucidating how each omicron mutation affects ACE2 binding. The enhanced ACE2 binding by the omicron RBD may facilitate the omicron variant's infection of the respiratory tracts where ACE2 expression level is low. Our study provides insights into the receptor recognition and tissue tropism of the omicron variant. IMPORTANCE Despite the scarcity of the SARS-CoV-2 receptor-human angiotensin-converting enzyme 2 (ACE2)-in the respiratory tract, the omicron variant efficiently infects the respiratory tract, causing rapid and widespread infections of COVID-19. The omicron variant contains extensive mutations in the receptor-binding domain (RBD) of its spike protein that recognizes human ACE2. Here, using a combination of biochemical and X-ray crystallographic approaches, we showed that the omicron RBD binds to ACE2 with enhanced affinity and also elucidated the role of each of the omicron mutations in ACE2 binding. The enhanced ACE2 binding by the omicron RBD may contribute to the omicron variant's new viral tropism in the respiratory tract despite the low level of ACE2 expression in the tissue. These findings help us to understand tissue tropism of the omicron variant and shed light on the molecular evolution of SARS-CoV-2.

Keywords: COVID-19; X-ray crystallography; angiotensin-converting enzyme 2; mutational hotspots; omicron variant; receptor-binding domain (RBD); receptor-binding motif (RBM).

FIG 1

Mutations in the receptor-binding motif (RBM) of the omicron variant. (A) Interface between prototypic RBM and ACE2. ACE2 is in green. RBD core structure is in cyan. RBM is in magenta. RBD residues that have undergone mutations from the prototypic strain to the omicron variant are labeled in red. Three mutational hot spots are highlighted as follows: hot spot-353 centers on Lys353 in ACE2, hot spot-31 centers on Lys31 in ACE2, and hot spot-ridge centers on the receptor-binding ridge in RBD. (B) Surface plasmon resonance (SPR) assay for ACE2/RBD binding. ACE2-Fc was coated to a protein A chip in a fixed direction, and individual RBDs flowed through. The data are presented as mean ± standard error of the mean (SEM) (n = 3) on a log scale. A Student’s two-tailed t test was performed to analyze the statistical difference between the prototypic RBD and each of the other RBDs. ***, P < 0.001; **, P < 0.01; *, P < 0.05. N.S., statistically not significant. See Table S1 in the supplemental material for detailed binding kinetics. (C) Reverse coating SPR assay for ACE2/RBD binding. Prototypic RBD-His or omicron RBD-His was coated to a CM5 chip in random orientations through chemical cross-linking, and His-tagged monomeric ACE2 flowed through. The data are presented as mean ± SEM (n = 3) on a log scale. A Student’s two-tailed t test was performed to analyze the statistical difference between the prototypic RBD and the omicron RBD. **, P < 0.01. See Table S1 in the supplemental material for detailed binding kinetics.

FIG 2

Overall structure of omicron chimeric RBD complexed with human ACE2. (A) Overall structure of omicron chimeric RBD complexed with ACE2. The omicron chimeric RBD contains the core structures (in cyan) from SARS-CoV-1 RBD and receptor-binding motif (RBM) (in magenta) from the prototypic RBD. ACE2 is in green. Two mutational hot spots in the RBM are shown. (B) Interface between omicron RBM and ACE2. Coloring and labeling are the same as Fig. 1A. (C) Unbiased composite omit map of the interface between the omicron RBD and ACE2. Contour level is 1σ.

FIG 3

Structural details at the mutational hot spot-353. (A) Interface between the prototypic RBM and ACE2. (B) Interface between the omicron RBM and ACE2. RBM residues that have undergone mutations from the prototypic strain to the omicron variant are labeled in red. Dotted lines indicate hydrogen bonds or salt bridges.

FIG 4

Structural details at the mutational hot spot-31. (A) Interface between the prototypic RBM and ACE2. (B) Interface between the omicron RBM and ACE2. Coloring and labeling are the same as Fig. 3.