Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants

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Abstract

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.

Abstract

SARS-CoV-2 Omicron variant evolves into multiple sub-variants. Here, authors evaluate the binding capacity of these sub-variants to human and animal ACE2s and reveal molecular bases for their receptor binding and broader interspecies recognition.

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Most cited references 70

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A Novel Coronavirus from Patients with Pneumonia in China, 2019

Na Zhu, Dingyu Zhang, Wenling Wang … (2020)

Summary In December 2019, a cluster of patients with pneumonia of unknown cause was linked to a seafood wholesale market in Wuhan, China. A previously unknown betacoronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia. Human airway epithelial cells were used to isolate a novel coronavirus, named 2019-nCoV, which formed a clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily. Different from both MERS-CoV and SARS-CoV, 2019-nCoV is the seventh member of the family of coronaviruses that infect humans. Enhanced surveillance and further investigation are ongoing. (Funded by the National Key Research and Development Program of China and the National Major Project for Control and Prevention of Infectious Disease in China.)

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UCSF Chimera--a visualization system for exploratory research and analysis.

Eric F. Pettersen, Thomas Goddard, Conrad Huang … (2004)

The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/. Copyright 2004 Wiley Periodicals, Inc.

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Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

Alexandra C Walls, Young-Jun Park, M. Alejandra Tortorici … (2020)

Summary The emergence of SARS-CoV-2 has resulted in >90,000 infections and >3,000 deaths. Coronavirus spike (S) glycoproteins promote entry into cells and are the main target of antibodies. We show that SARS-CoV-2 S uses ACE2 to enter cells and that the receptor-binding domains of SARS-CoV-2 S and SARS-CoV S bind with similar affinities to human ACE2, correlating with the efficient spread of SARS-CoV-2 among humans. We found that the SARS-CoV-2 S glycoprotein harbors a furin cleavage site at the boundary between the S1/S2 subunits, which is processed during biogenesis and sets this virus apart from SARS-CoV and SARS-related CoVs. We determined cryo-EM structures of the SARS-CoV-2 S ectodomain trimer, providing a blueprint for the design of vaccines and inhibitors of viral entry. Finally, we demonstrate that SARS-CoV S murine polyclonal antibodies potently inhibited SARS-CoV-2 S mediated entry into cells, indicating that cross-neutralizing antibodies targeting conserved S epitopes can be elicited upon vaccination.

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Author and article information

Contributors

Kefang Liu:

ORCID: http://orcid.org/0000-0001-9076-2647

liukf@im.ac.cn

Peiyi Wang:

ORCID: http://orcid.org/0000-0001-7737-181X

wangpy@sustech.edu.cn

George F. Gao:

ORCID: http://orcid.org/0000-0002-3869-615X

gaof@im.ac.cn

Jianxun Qi:

ORCID: http://orcid.org/0000-0002-9358-4732

jxqi@im.ac.cn

Journal

Journal ID (nlm-ta): Nat Commun

Journal ID (iso-abbrev): Nat Commun

Title: Nature Communications

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2041-1723

Publication date (Electronic): 21 July 2023

Publication date PMC-release: 21 July 2023

Publication date Collection: 2023

Volume: 14

Electronic Location Identifier: 4405

Affiliations

[1 ]GRID grid.9227.e, ISNI 0000000119573309, CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, , Chinese Academy of Sciences, ; Beijing, China

[2 ]GRID grid.410726.6, ISNI 0000 0004 1797 8419, University of Chinese Academy of Sciences, ; Beijing, China

[3 ]GRID grid.12527.33, ISNI 0000 0001 0662 3178, Department of Basic Medical Sciences, School of Medicine, , Tsinghua University, ; Beijing, China

[4 ]GRID grid.412545.3, ISNI 0000 0004 1798 1300, College of Veterinary Medicine, , Shanxi Agricultural University, ; Jinzhong, China

[5 ]GRID grid.9227.e, ISNI 0000000119573309, Research Network of Immunity and Health (RNIH), , Beijing Institutes of Life Science, Chinese Academy of Sciences, ; Beijing, China

[6 ]Shanxi Academy of Advanced Research and Innovation, Taiyuan, China

[7 ]GRID grid.437123.0, ISNI 0000 0004 1794 8068, Faculty of Health Sciences, , University of Macau, ; Macau, China

[8 ]GRID grid.458488.d, ISNI 0000 0004 0627 1442, Chinese National Microbiology Data Center (NMDC), , Institute of Microbiology, Chinese Academy of Sciences, ; Beijing, China

[9 ]GRID grid.508378.1, NHC Key Laboratory of Parasite and Vector Biology, , National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, ; Shanghai, China

[10 ]GRID grid.263817.9, ISNI 0000 0004 1773 1790, Cryo-EM Center, Department of Biology, , Southern University of Science and Technology, ; Shenzhen, China

[11 ]Beijing Life Science Academy, Beijing, China

Author information

Yufeng Xie http://orcid.org/0000-0001-9602-0003

Yeping Sun http://orcid.org/0000-0001-9977-9103

Xin Zhao http://orcid.org/0000-0002-2001-1343

Kefang Liu http://orcid.org/0000-0001-9076-2647

Peiyi Wang http://orcid.org/0000-0001-7737-181X

George F. Gao http://orcid.org/0000-0002-3869-615X

Jianxun Qi http://orcid.org/0000-0002-9358-4732

Article

Publisher ID: 39942

DOI: 10.1038/s41467-023-39942-z

PMC ID: 10362042

PubMed ID: 37479708

SO-VID: aa2de0f5-9670-4f98-afc9-38d430d0f0a1

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

History

Date received : 15 November 2022

Date accepted : 29 June 2023

Funding

Funded by: Strategic Priority Research Program of the Chinese Academy of Sciences(XDB37030204 and XDB29010202)

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ScienceOpen disciplines: Uncategorized

Keywords: sars-cov-2,cryoelectron microscopy,viral proteins,molecular biophysics

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ScienceOpen disciplines: Uncategorized

Keywords: sars-cov-2, cryoelectron microscopy, viral proteins, molecular biophysics

Structural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants

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Novel Coronavirus Disease COVID-19

Most cited references 70

A Novel Coronavirus from Patients with Pneumonia in China, 2019

UCSF Chimera--a visualization system for exploratory research and analysis.

Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein

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