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TitleStructural basis for receptor binding and broader interspecies receptor recognition of currently circulating Omicron sub-variants.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 4405, Year 2023
Publish dateJul 21, 2023
AuthorsZhennan Zhao / Yufeng Xie / Bin Bai / Chunliang Luo / Jingya Zhou / Weiwei Li / Yumin Meng / Linjie Li / Dedong Li / Xiaomei Li / Xiaoxiong Li / Xiaoyun Wang / Junqing Sun / Zepeng Xu / Yeping Sun / Wei Zhang / Zheng Fan / Xin Zhao / Linhuan Wu / Juncai Ma / Odel Y Li / Guijun Shang / Yan Chai / Kefang Liu / Peiyi Wang / George F Gao / Jianxun Qi /
PubMed AbstractMultiple 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 ...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.
External linksNat Commun / PubMed:37479708 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.58 - 3.29 Å
Structure data

33841

7yhw

EMDB-33841, PDB-7yhw:
Cryo-EM structure of SARS-CoV-2 Omicron BA.2.12.1 RBD in complex with human ACE2 (local refinement)
Method: EM (single particle) / Resolution: 3.09 Å

33870

7yj3

EMDB-33870, PDB-7yj3:
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with human ACE2 (local refinement)
Method: EM (single particle) / Resolution: 3.14 Å

34120

7yv8

EMDB-34120, PDB-7yv8:
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with golden hamster ACE2 (local refinement)
Method: EM (single particle) / Resolution: 2.94 Å

34138

7yvu

EMDB-34138, PDB-7yvu:
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with mouse ACE2 (local refinement)
Method: EM (single particle) / Resolution: 3.2 Å

34217

8gry

EMDB-34217, PDB-8gry:
Cryo-EM structure of SARS-CoV-2 Omicron BA.2 RBD in complex with rat ACE2 (local refinement)
Method: EM (single particle) / Resolution: 3.29 Å

34409

8h06

EMDB-34409, PDB-8h06:
Cryo-EM structure of SARS-CoV-2 Omicron BA.4/5 RBD in complex with human ACE2 (local refinement)
Method: EM (single particle) / Resolution: 2.66 Å

EMDB-34494: Cryo-EM map of SARS-CoV-2 Omicron BA.2 spike trimer in complex with human ACE2 (three-RBD-up conformation)
Method: EM (single particle) / Resolution: 3.09 Å

EMDB-34498: Cryo-EM map of SARS-CoV-2 Omicron BA.2.12.1 spike trimer in complex with human ACE2 (three-RBD-up conformation)
Method: EM (single particle) / Resolution: 3.19 Å

EMDB-34499: Cryo-EM map of SARS-CoV-2 Omicron BA.2 spike protein in complex with mouse ACE2
Method: EM (single particle) / Resolution: 3.02 Å

EMDB-34506: Cryo-EM map of SARS-CoV-2 Omicron BA.2 spike trimer in complex with rat ACE2
Method: EM (single particle) / Resolution: 3.01 Å

EMDB-34509: Cryo-EM map of SARS-CoV-2 Omicron BA.4/5 (N658S) spike trimer in complex with human ACE2 (three-RBD-up conformation)
Method: EM (single particle) / Resolution: 2.58 Å

EMDB-34510: Cryo-EM map of SARS-CoV-2 Omicron BA.2 spike trimer in complex with golden hamster ACE2
Method: EM (single particle) / Resolution: 2.96 Å

PDB-8h5c:
Structure of SARS-CoV-2 Omicron BA.2.75 RBD in complex with human ACE2
Method: X-RAY DIFFRACTION / Resolution: 2.9 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-ZN:
Unknown entry

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
  • mesocricetus auratus (golden hamster)
  • mus musculus (house mouse)
  • rattus norvegicus (Norway rat)
KeywordsHYDROLASE/VIRAL PROTEIN / SARS-CoV-2 / Omicron BA.2.12.1 / spike protein / VIRAL PROTEIN / HYDROLASE-VIRAL PROTEIN complex / Omicron BA.2 / Omicron BA.4/5 / Omicron BA.2.75 / hACE2

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