The currently circulating Omicron sub-variants are the SARS-CoV-2 strains with the highest number of known mutations. Herein, we found that human angiotensin-converting enzyme 2 (hACE2) binding ...affinity to the receptor-binding domains (RBDs) of the four early Omicron sub-variants (BA.1, BA.1.1, BA.2, and BA.3) follows the order BA.1.1 > BA.2 > BA.3 ≈ BA.1. The complex structures of hACE2 with RBDs of BA.1.1, BA.2, and BA.3 reveal that the higher hACE2 binding affinity of BA.2 than BA.1 is related to the absence of the G496S mutation in BA.2. The R346K mutation in BA.1.1 majorly affects the interaction network in the BA.1.1 RBD/hACE2 interface through long-range alterations and contributes to the higher hACE2 affinity of the BA.1.1 RBD than the BA.1 RBD. These results reveal the structural basis for the distinct hACE2 binding patterns among BA.1.1, BA.2, and BA.3 RBDs.
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•Omicron BA.1.1 and BA.2 show higher binding strength to hACE2 than the prototype and BA.1•Details in the binding interface of BA.1.1, BA.2, and BA.3.RBD with hACE2 are deciphered•R346K in BA.1.1 RBD enhances the interaction with hACE2 through long-range alterations
The biochemical and structural analysis of the human angiotensin-converting enzyme-2 (ACE2, the receptor for SARS-CoV-2 viral entry) and the receptor-binding domain (RBD) of four Omicron sub-variants—BA.1, BA.1.1, BA.2, and BA.3—helps to reveal the structural basis of differences in sub-variant binding affinities and the impact of RBD mutations.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading worldwide, causing a global pandemic. Bat-origin RaTG13 is currently the most phylogenetically related virus. Here we ...obtained the complex structure of the RaTG13 receptor binding domain (RBD) with human ACE2 (hACE2) and evaluated binding of RaTG13 RBD to 24 additional ACE2 orthologs. By substituting residues in the RaTG13 RBD with their counterparts in the SARS-CoV-2 RBD, we found that residue 501, the major position found in variants of concern (VOCs) 501Y.V1/V2/V3, plays a key role in determining the potential host range of RaTG13. We also found that SARS-CoV-2 could induce strong cross-reactive antibodies to RaTG13 and identified a SARS-CoV-2 monoclonal antibody (mAb), CB6, that could cross-neutralize RaTG13 pseudovirus. These results elucidate the receptor binding and host adaption mechanisms of RaTG13 and emphasize the importance of continuous surveillance of coronaviruses (CoVs) carried by animal reservoirs to prevent another spillover of CoVs.
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•The complex structure of RaTG13 RBD with hACE2 was determined•Binding of RaTG13 RBD to 24 additional ACE2 orthologs was evaluated•Residue 501 plays a key role in determining the potential host range of RaTG13•SARS-CoV-2 induces strong cross-protective antibodies to RaTG13 RBD
Structural and molecular analysis of the receptor binding domain of RaTG13, a coronavirus phylogenetically closely related to SARS-CoV-2, bound to the human receptor ACE2 as well as ACE2 orthologs in 24 other species provides a framework to understand its host range as well as the basis of antibody cross-reactivity between the two viruses.
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the recent pandemic COVID-19, is reported to have originated from bats, with its intermediate host ...unknown to date. Here, we screened 26 animal counterparts of the human ACE2 (hACE2), the receptor for SARS-CoV-2 and SARS-CoV, and found that the ACE2s from various species, including pets, domestic animals and multiple wild animals, could bind to SARS-CoV-2 receptor binding domain (RBD) and facilitate the transduction of SARS-CoV-2 pseudovirus. Comparing to SARS-CoV-2, SARS-CoV seems to have a slightly wider range in choosing its receptor. We further resolved the cryo-electron microscopy (cryo-EM) structure of the cat ACE2 (cACE2) in complex with the SARS-CoV-2 RBD at a resolution of 3 Å, revealing similar binding mode as hACE2 to the SARS-CoV-2 RBD. These results shed light on pursuing the intermediate host of SARS-CoV-2 and highlight the necessity of monitoring susceptible hosts to prevent further outbreaks.
Multiple SARS-CoV-2 Omicron sub-variants, such as BA.2, BA.2.12.1, BA.4, and BA.5, emerge one after another. BA.5 has become the dominant strain worldwide. Additionally, BA.2.75 is significantly ...increasing in some countries. Exploring their receptor binding and interspecies transmission risk is urgently needed. Herein, we examine the binding capacities of human and other 28 animal ACE2 orthologs covering nine orders towards S proteins of these sub-variants. The binding affinities between hACE2 and these sub-variants remain in the range as that of previous variants of concerns (VOCs) or interests (VOIs). Notably, R493Q reverse mutation enhances the bindings towards ACE2s from humans and many animals closely related to human life, suggesting an increased risk of cross-species transmission. Structures of S/hACE2 or RBD/hACE2 complexes for these sub-variants and BA.2 S binding to ACE2 of mouse, rat or golden hamster are determined to reveal the molecular basis for receptor binding and broader interspecies recognition.
African swine fever virus (ASFV) is the causative agent of African swine fever, a highly fatal hemorrhagic disease of pigs, which has resulted in great economic losses to the global pork industry, ...especially in Asia. ASFV particles are comprised of multiple layers encompassing the genomic DNA. Though the capsid structure has been determined, very little is known about the structure of the core shell. The precursor polyprotein pp62 is the structural component of the core shell that gives rise to the p35 and p15 proteins. Herein, we describe the crystal structure of p15 at a resolution of 2.2 Å. The structure of p15 exhibits as a trimeric conformation that is mainly mediated by intermolecular disulfide bonds and supported by multiple hydrogen bond interactions. The button conformation on the surface of adjacent molecules may also play a role in trimeric formation of the ASFV p15. The center of the p15 trimer exhibits opposite electrostatic characteristics on each side. These findings benefit our understanding of ASFV core shell assembly and will aid in the design of antiviral drugs and vaccines.
•Scientific questionNone of the structures of these core shell proteins have been reported, and the lack of information concerning the core shell architecture has restricted our understanding of ASFV virus assembly and vaccine design.•Evidence before this studyThe core shell is comprised of the products of two precursor polyproteins: pp220 and pp62.pp220 gives rise to p150, p37, p34, p14, and p5, while pp62 gives rise to p35, p15, and p8, after proteolytic processing by the ASFV-encoded pS273R protease of the SUMO-1-specific protease family.•New findingsIn this study, the crystal structure of p15 was determined at a resolution of 2.2 Å. The solved p15 structure presented as a trimer. The p15 trimer is formed via an intermolecular disulfide bond between C8 and C29 of two adjacent molecules. The center of the p15 trimer exhibits opposite electrostatic characteristics on each side.•Significance of the studyOur study provides the detail conformation of a core shell protein, p15, which is composed of an α-helix head and β-sheet tail. These findings benefit our understanding of the mechanisms of ASFV core shell assembly and will aid in the future design of anti-viral drugs or vaccines.
To determine factors associated with lateralization in primary aldosteronism (PA). The clinical data for PA patients hospitalized at the First Affiliated Hospital of Guangxi Medical University from ...October 2016 to March 2021 were included in this study. They were classified according to results derived from computed tomography (CT): bilaterally normal nodules (no typical nodules were found in either adrenal glands, only changes in unilateral adrenal hyperplasia thickening or bilateral adrenal hyperplasia thickening), unilateral nodules (typical nodule appears in unilateral adrenal gland, and there are no abnormalities in the contralateral adrenal gland or only thickening of unilateral adrenal hyperplasia) and bilateral nodules (typical nodule like changes in bilateral adrenal glands). Multivariate logistic regression and receiver operating characteristic (ROC) were used to analyze the factors associated with lateralization of PA and consistencies between adrenal CT images and adrenal venous sampling (AVS) results. A total of 269 patients with PA were recruited, with an average age of 46 years and 112 cases had typical nodules. Results from CT scans revealed that there were 49 bilateral normal cases, 177 cases were unilateral abnormal and 43 cases were bilateral abnormal. In all of the PA patients, multifactorial logistic regression analysis showed that the maximum systolic blood pressure (OR = 1.03, P < .001), history of stroke (OR = 2.61, P = .028), and typical nodules (OR = 1.9, P = .017) were all relevant factors in unilateral primary aldosteronism (UPA). In the unilateral nodule group, multivariate logistic regression analysis suggested that maximum systolic blood pressure (OR = 1.03, P < .001) and typical nodules (OR = 2.37, P = .008) were the related factors for UPA. However, the consistency between adrenal CT and AVS was only 40.68%, while maximum systolic blood pressure (OR = 1.02, P < .001) and plasma aldosterone renin ratio (OR = 1.001, P = .027) were the relevant consistent factors between AVS and CT results. Maximum systolic blood pressure, typical nodules, and history of stroke are important factors to consider when screening for UPA. It is recommended to combine medical history and imaging findings when looking at different subgroups before a clinical decision is made. Patients with PA in the absence of lesions or bilateral lesions on CT should be diagnosed by AVS as far as possible.
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a major threat to global health. Although varied ...SARS-CoV-2-related coronaviruses have been isolated from bats and SARS-CoV-2 may infect bat, the structural basis for SARS-CoV-2 to utilize the human receptor counterpart bat angiotensin-converting enzyme 2 (bACE2) for virus infection remains less understood. Here, we report that the SARS-CoV-2 spike protein receptor binding domain (RBD) could bind to bACE2 from
(bACE2-Rm) with substantially lower affinity compared with that to the human ACE2 (hACE2), and its infectivity to host cells expressing bACE2-Rm was confirmed with pseudotyped SARS-CoV-2 virus and SARS-CoV-2 wild virus. The structure of the SARS-CoV-2 RBD with the bACE2-Rm complex was determined, revealing a binding mode similar to that of hACE2. The analysis of binding details between SARS-CoV-2 RBD and bACE2-Rm revealed that the interacting network involving Y41 and E42 of bACE2-Rm showed substantial differences with that to hACE2. Bats have extensive species diversity and the residues for RBD binding in bACE2 receptor varied substantially among different bat species. Notably, the Y41H mutant, which exists in many bats, attenuates the binding capacity of bACE2-Rm, indicating the central roles of Y41 in the interaction network. These findings would benefit our understanding of the potential infection of SARS-CoV-2 in varied species of bats.
ABSTRACT
SARS-CoV-2 has been expanding its host range, among which the white-tailed deer (WTD),
Odocoileus virginianus,
became the first wildlife species infected on a large scale and might serve as ...a host reservoir for variants of concern (VOCs) in case no longer circulating in humans. In this study, we comprehensively assessed the binding of the WTD angiotensin-converting enzyme 2 (ACE2) receptor to the spike (S) receptor-binding domains (RBDs) from the SARS-CoV-2 prototype (PT) strain and multiple variants. We found that WTD ACE2 could be broadly recognized by all of the tested RBDs. We further determined the complex structures of WTD ACE2 with PT, Omicron BA.1, and BA.4/5 S trimer. Detailed structural comparison revealed the important roles of RBD residues on 486, 498, and 501 sites for WTD ACE2 binding. This study deepens our understanding of the interspecies transmission mechanisms of SARS-CoV-2 and further addresses the importance of constant monitoring on SARS-CoV-2 infections in wild animals.
IMPORTANCE
Even if we manage to eliminate the virus among humans, it will still circulate among wildlife and continuously be transmitted back to humans. A recent study indicated that WTD may serve as reservoir for nearly extinct SARS-CoV-2 strains. Therefore, it is critical to evaluate the binding abilities of SARS-CoV-2 variants to the WTD ACE2 receptor and elucidate the molecular mechanisms of binding of the RBDs to assess the risk of spillback events.
Even if we manage to eliminate the virus among humans, it will still circulate among wildlife and continuously be transmitted back to humans. A recent study indicated that WTD may serve as reservoir for nearly extinct SARS-CoV-2 strains. Therefore, it is critical to evaluate the binding abilities of SARS-CoV-2 variants to the WTD ACE2 receptor and elucidate the molecular mechanisms of binding of the RBDs to assess the risk of spillback events.
After binding to its cell surface receptor angiotensin converting enzyme 2 (ACE2), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) enters the host cell through directly fusing with ...plasma membrane (cell surface pathway) or undergoing endocytosis traveling to lysosome/late endosome for membrane fusion (endocytic pathway). However, the endocytic entry regulation by host cell remains elusive. Recent studies show ACE2 possesses a type I PDZ binding motif (PBM) through which it could interact with a PDZ domain-containing protein such as sorting nexin 27 (SNX27). In this study, we determined the ACE2-PBM/SNX27-PDZ complex structure, and, through a series of functional analyses, we found SNX27 plays an important role in regulating the homeostasis of ACE2 receptor. More importantly, we demonstrated SNX27, together with retromer complex (the core component of the endosomal protein sorting machinery), prevents ACE2/virus complex from entering lysosome/late endosome, resulting in decreased viral entry in cells where the endocytic pathway dominates. The ACE2/virus retrieval mediated by SNX27-retromer could be considered as a countermeasure against invasion of ACE2 receptor-using SARS coronaviruses.
The spike protein of SARS-CoV-2 has been a promising target for developing vaccines and therapeutics due to its crucial role in the viral entry process. Previously reported cryogenic electron ...microscopy (cryo-EM) structures have revealed that free fatty acids (FFA) bind with SARS-CoV-2 spike protein, stabilizing its closed conformation and reducing its interaction with the host cell target in vitro. Inspired by these, we utilized a structure-based virtual screening approach against the conserved FFA-binding pocket to identify small molecule modulators of SARS-CoV-2 spike protein, which helped us identify six hits with micromolar binding affinities. Further evaluation of their commercially available and synthesized analogs enabled us to discover a series of compounds with better binding affinities and solubilities. Notably, our identified compounds exhibited similar binding affinities against the spike proteins of the prototypic SARS-CoV-2 and a currently circulating Omicron BA.4 variant. Furthermore, the cryo-EM structure of the compound SPC-14 bound spike revealed that SPC-14 could shift the conformational equilibrium of the spike protein toward the closed conformation, which is human ACE2 (hACE2) inaccessible. Our identified small molecule modulators targeting the conserved FFA-binding pocket could serve as the starting point for the future development of broad-spectrum COVID-19 intervention treatments.
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