8WDS

Crystal structure of BF.7 RBD complexed with human ACE2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Key mechanistic features of the trade-off between antibody escape and host cell binding in the SARS-CoV-2 Omicron variant spike proteins.

Li, W.Xu, Z.Niu, T.Xie, Y.Zhao, Z.Li, D.He, Q.Sun, W.Shi, K.Guo, W.Chang, Z.Liu, K.Fan, Z.Qi, J.Gao, G.F.

(2024) EMBO J 43: 1484-1498

  • DOI: https://doi.org/10.1038/s44318-024-00062-z
  • Primary Citation of Related Structures:  
    8WDR, 8WDS, 8WDY, 8WDZ, 8WE0, 8WE1, 8WE4

  • PubMed Abstract: 

    Since SARS-CoV-2 Omicron variant emerged, it is constantly evolving into multiple sub-variants, including BF.7, BQ.1, BQ.1.1, XBB, XBB.1.5 and the recently emerged BA.2.86 and JN.1. Receptor binding and immune evasion are recognized as two major drivers for evolution of the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein. However, the underlying mechanism of interplay between two factors remains incompletely understood. Herein, we determined the structures of human ACE2 complexed with BF.7, BQ.1, BQ.1.1, XBB and XBB.1.5 RBDs. Based on the ACE2/RBD structures of these sub-variants and a comparison with the known complex structures, we found that R346T substitution in the RBD enhanced ACE2 binding upon an interaction with the residue R493, but not Q493, via a mechanism involving long-range conformation changes. Furthermore, we found that R493Q and F486V exert a balanced impact, through which immune evasion capability was somewhat compromised to achieve an optimal receptor binding. We propose a "two-steps-forward and one-step-backward" model to describe such a compromise between receptor binding affinity and immune evasion during RBD evolution of Omicron sub-variants.


  • Organizational Affiliation

    CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2
A, C
805Homo sapiensMutation(s): 0 
Gene Names: ACE2
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: 3Go to GlyGen: Q9BYF1-1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1
B, D
247Severe acute respiratory syndrome coronavirus 2Mutation(s): 18 
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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P0DTC2-1
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
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
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
F
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth B]
L [auth C]
M [auth C]
H [auth A],
I [auth A],
J [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A],
K [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.695α = 90
b = 137.349β = 90
c = 154.765γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-07-24 
  • Deposition Author(s): Li, W., Xie, Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release