Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor
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Abstract
A new and highly pathogenic coronavirus (severe acute respiratory syndrome coronavirus-2, SARS-CoV-2) caused an outbreak in Wuhan city, Hubei province, China, starting from December 2019 that quickly spread nationwide and to other countries around the world 1-3. Here, to better understand the initial step of infection at an atomic level, we determined the crystal structure of the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 bound to the cell receptor ACE2. The overall ACE2-binding mode of the SARS-CoV-2 RBD is nearly identical to that of the SARS-CoV RBD, which also uses ACE2 as the cell receptor 4. Structural analysis identified residues in the SARS-CoV-2 RBD that are essential for ACE2 binding, the majority of which either are highly conserved or share similar side chain properties with those in the SARS-CoV RBD. Such similarity in structure and sequence strongly indicate convergent evolution between the SARS-CoV-2 and SARS-CoV RBDs for improved binding to ACE2, although SARS-CoV-2 does not cluster within SARS and SARS-related coronaviruses 1-3,5. The epitopes of two SARS-CoV antibodies that target the RBD are also analysed for binding to the SARS-CoV-2 RBD, providing insights into the future identification of cross-reactive antibodies.
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The SARS-CoV-2 receptor-binding domain amino acid sequence extends from residue Thr333 to residue Gly526.
“This amino acid sequence extends from residue Thr333 to residue Gly526 [28].”
From Effects of Mangiferin on LPS-Induced Inflammation and SARS-CoV-2 Viral Adsorption in Human Lung Cells (2022) · cites this paper as [28]
In the paper’s main text, the final structural model contains SARS-CoV-2 RBD residues Thr333–Gly526. But the authors say they expressed an RBD spanning Arg319–Phe541, so Thr333–Gly526 describes the residues included in the model, not the full amino acid sequence of the RBD. (LLM, conf=0.90)
Experimental — accuracy not yet measuredACE2 had been identified as the receptor for SARS-CoV and SARS-CoV-2.
“Importantly, ACE2 (angiotensin-converting enzyme 2) had been identified as the receptor for SARS-CoV 4,5 and SARS-CoV-2.”
From COVID-19, Myocarditis and Pericarditis (2023) · cites this paper as [7]
When binding to hACE2, spike amino acid F486 interacts with hACE2 residues L79, M82 and Y83, which collectively comprise a hotspot for ACE2 differences between mammalian species.
“When binding to hACE2, spike amino acid F486 interacts with hACE2 residues L79, M82 and Y83, which collectively comprise a hotspot for ACE2 differences between mammalian species13.”
From Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa (2022) · cites this paper as [13]
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“This amino acid sequence extends from residue Thr333 to residue Gly526 [28].”
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- Authors
- Lan, J., Ge, J., Yu, J., Shan, S., Zhou, H., Fan, S., Zhang, Q., Shi, X., Wang, Q., Zhang, L., & Wang, X.
- Affiliations
- Tsinghua University (CN)
- Chinese Academy of Sciences (CN)
- Corresponding author
- Zhang, Qi
- Zhang, Linqi
- Wang, Xinquan
- ORCID
- Venue
- Nature
- Published
- 2020-03-30
- Volume
- 581
- Issue
- 7807
- Pages
- 215-220
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W3014067025
- Cited by
- 5,983
- References
- 10
- Citations by year
- 2026: 207 · 2025: 404 · 2024: 573 · 2023: 797 · 2022: 1237 · 2021: 1678 · 2020: 1076 · 2012: 2
- FWCI
- 152.41
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Salt Science Research Foundation
- Tencent
- Tsinghua University (20201080053)
- Beijing Municipal Science and Technology Commission (171100000517-001 and -003)
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University
- Topics
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Keywords
- SARS-CoV-2, spike protein, receptor binding domain, ACE2, crystal structure, SARS-CoV, convergent evolution, antibody epitopes, cross-reactive antibodies, viral entry, binding site residues
- MeSH terms
- Protein Domains, Betacoronavirus, Angiotensin-Converting Enzyme 2, SARS-CoV-2, Amino Acid Sequence, Epitopes, Binding Sites, Humans, Hydrogen Bonding, Peptidyl-Dipeptidase A, Models, Molecular, Protein Binding, Receptors, Virus, Salts, Water, Sequence Alignment, Conserved Sequence, Crystallography, X-Ray, Evolution, Molecular, Severe acute respiratory syndrome-related coronavirus, Antibodies, Neutralizing, Spike Glycoprotein, Coronavirus
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