Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2

Abstract

The coronavirus disease 2019 (COVID-19) pandemic continues worldwide with many variants arising, some of which are variants of concern (VOCs). A recent VOC, omicron (B.1.1.529), which obtains a large number of mutations in the receptor-binding domain (RBD) of the spike protein, has risen to intense scientific and public attention. Here, we studied the binding properties between the human receptor ACE2 (hACE2) and the VOC RBDs and resolved the crystal and cryoelectron microscopy structures of the omicron RBD-hACE2 complex as well as the crystal structure of the delta RBD-hACE2 complex. We found that, unlike alpha, beta, and gamma, omicron RBD binds to hACE2 at a similar affinity to that of the prototype RBD, which might be due to compensation of multiple mutations for both immune escape and transmissibility. The complex structures of omicron RBD-hACE2 and delta RBD-hACE2 reveal the structural basis of how RBD-specific mutations bind to hACE2.

Keywords: RBD; VOCs; delta; hACE2; omicron; receptor-binding domain; structure; variants of concern.

Graphical abstract

Figure 1

Mutation mapping and sequence alignment of RBDs from prototype SARS-CoV-2, VOCs, and pangolin-origin GD/1/2019 (A) Architecture of SARS-CoV-2 genome and S protein and substitution mapping of RBDs from prototype SARS-CoV-2, VOCs, and pangolin-origin GD/1/2019. (B) Sequence alignment of abovementioned RBDs. Interacting residues of prototype SARS-CoV-2 RBD to hACE2 are labeled with black triangles. The alignment is performed by T-COFFEE and visualized by ESPript 3.0. See also Figure S1.

Figure S1

Phylogenetic analysis of representative SARS-CoV-2, related VOCs, and GD/1/2019, Related to Figure 1 Phylogenetic trees are depicted for nucleotide sequences of the full genome (A) and RBD (B).

Figure 2

Binding characteristics and transduction of SARS-CoV-2 VOCs (A) BHK-21 cells stably expressing GFP and hACE2 were incubated with His-tagged RBDs from prototype SARS-CoV-2, VOCs, and pangolin-origin GD/1/2019. Allophycocyanin (APC)-conjugated anti-His antibodies were used to detect the His-tagged protein binding to the cells. Representative results from three experiments are shown. The frequency of RBD-binding positive cells in ACE2-GFP positive cells are labeled in the upright corner. (B) Transduction efficiency of pseudotyped prototype SARS-CoV-2, D614G variant, and VOCs. The GFP-positive cells were quantified with CQ1 confocal image cytometer (Yokogawa), and representative results from three experiments are shown. Statistical significance was analyzed with a t test comparison between VOCs and D614G. (C) SPR characterization of RBDs from prototype SARS-CoV-2, VOCs, and pangolin-origin GD/1/2019 interacting with hACE2. Dissociation constant (K_D) indicates mean ± SD of three independent replicates. Actual and fitted curves are colored in black and red, respectively. See also Figure S2.

Figure S2

Entry of the pseudovirus of prototype SARS-CoV-2 and its VOCs into Vero cells, Related to Figure 2 Green fluorescent Vero cells indicate pseudovirus-transducing cells. Untransfected Vero cells were used as negative controls.

Figure S3

Cryo-EM structrual analysis of hACE2-omicron RBD, Related to Figure 3 (A) A representative cryo-EM micrograph of hACE2-Omicron RBD. Scale bar, 50 nm. (B) 2D class average images of hACE2-Omicron RBD. (C) A brief workflow of cryo-EM image processing and reconstruction. (D) Euler angle distribution of the final reconstruction. (E) The FSC curve for the reconstruction. (F) Local resolution distribution for the density map of hACE2-Omicron RBD.

Figure 3

Overall architecture and interaction network of hACE2-omicron RBD and hACE2-delta RBD complexes (A–C) Overall architecture of hACE2-omicron RBD crystal structure (A) and cryo-EM structure (B) and crystal structure of hACE2-delta RBD complex (C). (D) Interaction patches in crystal structure of hACE2-omicron RBD. Side chains of interacting residues on hACE2 (green) and omicron RBD (pink) are shown as sticks and labeled appropriately. Yellow, red, and blue dashes present H bond, π-π stacking interaction, and salt bridges, respectively. (E) Interaction patches in crystal structure of hACE2-delta RBD. Side chains of interacting residues on hACE2 (green) and omicron RBD (purple) are shown as sticks. Yellow, red, and blue dashes present H bond, π-π stacking interaction, and salt bridges, respectively. See also Figures S3, S4, and S5.

Figure S4

Representative densities and atomic models, Related to Figure 3 Representative densities and atomic models of Omicron RBD-hACE2 complex structures solved through cryo-EM (A) and X-ray (B) were shown. hACE2 was shown as green and Omicron RBD was colored by salmon. The representative densities and atomic models of Delta RBD-hACE2 complex structures determined by cryo-EM (PBD: 7V7V) (C) and X-ray (D) were shown. hACE2 was also shown as green and Delta RBD was labeled by magenta.

Figure S5

Overall structure comparison of hACE2 with VOC RBDs and GD/1/2019 RBD, Related to Figure 3 (A-C) The crystal structure (A) and cryo-EM structure (B) of Omicron RBD-hACE2 complex and crystal structure of Delta RBD-hACE2 complex are compared with prototype RBD-hACE2 complex and labeled by salmon. Both crystal structure and cryo-EM structure of Omicron RBD-hACE2 complex were colored by salmon. Delta RBD-hACE2 complex was labeled by magenta. Prototype RBD-hACE2 complex was labeled by white. (D and E) The structural comparations between crystal structure and cryo-EM structure of Omicron RBD-hACE2 complex (D) and Delta RBD-hACE2 complex (E). The cryo-EM of both Omicron RBD-hACE2 complex and Delta RBD-hACE2 complex were colored by white and the corresponding crystal structures were labeled by salmon and magenta, respectively.

Figure 4

The RBMs and different residues on the RBDs (A–D) The binding surfaces of hACE2 with prototype RBD (A), omicron RBD (B), delta RBD (C), and GD/1/2019 RBD (D) were labeled in cyan, salmon, magenta, and light blue, respectively. (E and F) Nine different residues on hACE2 binding interface between omicron RBD and prototype RBD were labeled. (I and J) Electrostatic surface view of prototype SARS-CoV-2 RBD and omicron RBD. The first panel represents the top view. The others are yielded by rotation of the former panel along a horizontal axis. (K and L) The different residues on the RBMs between VOCs and prototype are labeled. See also Figure S6.

Figure 5

Structural comparison of prototype RBD-hACE2 and omicron RBD-hACE2 (A–H) The nine substitutions on the binding surface of RBD are shown. The residues in the prototype RBD are shown as cyan sticks and the residues in the omicron RBD are shown as green sticks. The yellow dashes represent H bond and salt bridges between prototype RBD and hACE2. The red dashes represent H bond and salt bridges between omicron RBD and hACE2. H-bond interactions were analyzed at a cutoff of 3.5 Å.

Figure S6

Electrostatic surface view, Related to Figure 4 Electrostatic surface view of SARS-CoV-2 VOCs Alpha, Beta, Gamma and Delta RBDs and GD/1/2019 RBD. The first panel represents the top view. The others are yielded by rotation of the former panel along a horizontal axis.