Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2

Abstract

Angiotensin-converting enzyme 2 (ACE2) is the cellular receptor for severe acute respiratory syndrome-coronavirus (SARS-CoV) and the new coronavirus (SARS-CoV-2) that is causing the serious coronavirus disease 2019 (COVID-19) epidemic. Here, we present cryo-electron microscopy structures of full-length human ACE2 in the presence of the neutral amino acid transporter B⁰AT1 with or without the receptor binding domain (RBD) of the surface spike glycoprotein (S protein) of SARS-CoV-2, both at an overall resolution of 2.9 angstroms, with a local resolution of 3.5 angstroms at the ACE2-RBD interface. The ACE2-B⁰AT1 complex is assembled as a dimer of heterodimers, with the collectrin-like domain of ACE2 mediating homodimerization. The RBD is recognized by the extracellular peptidase domain of ACE2 mainly through polar residues. These findings provide important insights into the molecular basis for coronavirus recognition and infection.

Fig. 1. Overall structure of the ACE2-B⁰AT1 complex.

(A) Representative size exclusion chromatography purification profile of full-length human ACE2 in complex with B⁰AT1. UV, ultraviolet; mAU, milli–absorbance units; MWM, molecular weight marker. (B) Cryo-EM map of the ACE2-B⁰AT1 complex. The map is generated by merging the focused refined maps shown in fig. S2. Protomer A of ACE2 (cyan), protomer B of ACE2 (blue), protomer A of B⁰AT1 (pink) and protomer B of B⁰AT1 (gray) are shown. (C) Cartoon representation of the atomic model of the ACE2-B⁰AT1 complex. The glycosylation moieties are shown as sticks. The complex is colored by subunits, with the PD and CLD in one ACE2 protomer colored cyan and blue, respectively. (D) An open conformation of the ACE2-B⁰AT1 complex. The two PDs, which contact each other in the closed conformation, are separated in the open conformation.

Fig. 2. Dimerization interface of ACE2.

(A) ACE2 dimerizes through two interfaces, the PD and the neck domain. The regions enclosed by the cyan and red dashed lines are illustrated in detail in (B) and (C), respectively. (B) The primary dimeric interface is through the neck domain in ACE2. Polar interactions are represented by red dashed lines. (C) A weaker interface between PDs of ACE2. The only interaction is between Gln¹³⁹ and Gln^175′, which are highlighted as spheres. The polar residues that may contribute to the stabilization of Gln¹³⁹ are shown as sticks. (D) The PDs no longer contact each other in the open state. Single-letter abbreviations for the amino acid residues used in the figures are as follows: C, Cys; D, Asp; E, Glu; F, Phe; H, His; K, Lys; L, Leu; M, Met; N, Asn; Q, Gln; R, Arg; S, Ser; T, Thr; V, Val; and Y, Tyr.

Fig. 3. Overall structure of the RBD-ACE2-B⁰AT1 complex.

(A) Cryo-EM map of the RBD-ACE2-B⁰AT1 complex. The overall reconstruction of the ternary complex at 2.9 Å is shown on the left. The inset shows the focused refined map of RBD. The color scheme is the same as that in Fig. 1B, with the addition of red and gold, which represent RBD protomers. (B) Overall structure of the RBD-ACE2-B⁰AT1 complex. The color scheme is the same as that in Fig. 1C. The glycosylation moieties are shown as sticks.

Fig. 4. Interactions between SARS-CoV-2-RBD and ACE2.

(A) The PD of ACE2 mainly engages the α1 helix in the recognition of the RBD. The α2 helix and the linker between β3 and β4 also contribute to the interaction. Only one RBD-ACE2 is shown. (B to D) Detailed analysis of the interface between SARS-CoV-2-RBD and ACE2. Polar interactions are indicated by red dashed lines. NAG, N-acetylglucosamine.

Fig. 5. Interface comparison between SARS-CoV-2-RBD and SARS-CoV-RBD with ACE2.

(A) Structural alignment for the SARS-CoV-2-RBD and SARS-CoV-RBD. The structure of the ACE2-PD and the SARS-CoV-RBD complex (PDB 2AJF) is superimposed on our cryo-EM structure of the ternary complex relative to the RBDs. The regions enclosed by the purple, blue, and red dashed lines are illustrated in detail in (B) to (D), respectively. SARS-CoV-2-RBD and the PD in our cryo-EM structure are colored orange and cyan, respectively; SARS-CoV-RBD and its complexed PD are colored green and gold, respectively. (B to D) Variation of the interface residues between SARS-CoV-2-RBD (labeled in brown) and SARS-CoV-RBD (labeled in green).