8XYE | pdb_00008xye

Crystal structure of SARS-CoV-2 BA.4 RBD and human ACE2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 
    0.242 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Receptor binding mechanism and immune evasion capacity of SARS-CoV-2 BQ.1.1 lineage.

Wang, C.Zhang, Y.Yang, C.Ren, W.Qiu, C.Fan, S.Ding, Q.Lan, J.

(2024) Virology 600: 110241-110241

  • DOI: https://doi.org/10.1016/j.virol.2024.110241
  • Primary Citation of Related Structures:  
    8XY9, 8XYE, 8XYG

  • PubMed Abstract: 

    The global spread of COVID-19 remains a significant threat to human health. The SARS-CoV-2 BQ.1.1 lineage, including BA.5.2, BF.7, BQ.1 and BQ.1.1, caused a new soaring of infection cases due to rapid transmission. However, the receptor binding mechanism and immune evasion capacity of these variants need to be explored further. Our study found that while the BA.5.2, BF.7 and BQ.1.1 variants pseudovirus had similar cell entry efficiency, the BF.7 and BQ.1.1 RBD bound to human ACE2 (hACE2) with a slightly stronger affinity than the BA.5.2 RBD. Structural analysis revealed R346T, K444T, and N460K mutations altered RBD-hACE2 binding interface details and surface electrostatic potential of BQ.1.1 RBD. Serum neutralization tests showed BQ.1.1 variant had stronger immune evasion capacity than BA.5.2 and BF.7 variants. Our findings illustrated the receptor binding mechanism and serological neutralization activity of the BA.5.2, BF.7 and BQ.1.1 variants, which verified the necessity for further antibody therapy optimization and vaccination development.


  • Organizational Affiliation
    • School of Biomedical Sciences, Hunan University, Changsha, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Processed angiotensin-converting enzyme 2A [auth B],
D [auth A]
598Homo sapiensMutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
EC: 3.4.17 (UniProt), 3.4.17.23 (UniProt)
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 protein S1B [auth C],
C [auth D]
194Severe acute respiratory syndrome coronavirus 2Mutation(s): 16 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F, G
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free:  0.242 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.468α = 90
b = 165.822β = 102.18
c = 98.981γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-04-16
    Changes: Database references