7DRV

Structural basis of SARS-CoV-2-closely-related bat coronavirus RaTG13 to hACE2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

Starting Model: experimental
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Literature

Binding and molecular basis of the bat coronavirus RaTG13 virus to ACE2 in humans and other species.

Liu, K.Pan, X.Li, L.Yu, F.Zheng, A.Du, P.Han, P.Meng, Y.Zhang, Y.Wu, L.Chen, Q.Song, C.Jia, Y.Niu, S.Lu, D.Qiao, C.Chen, Z.Ma, D.Ma, X.Tan, S.Zhao, X.Qi, J.Gao, G.F.Wang, Q.

(2021) Cell 184: 3438-3451.e10

  • DOI: https://doi.org/10.1016/j.cell.2021.05.031
  • Primary Citation of Related Structures:  
    7DRV

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2A,
C [auth B]
596Homo sapiensMutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1 
Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1
GTEx:  ENSG00000130234 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYF1
Glycosylation
Glycosylation Sites: 5Go to GlyGen: Q9BYF1-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinB [auth C],
D
223Bat coronavirus RaTG13Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.09 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.276α = 90
b = 122.875β = 95.067
c = 110.742γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-25
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description