8I4E

Omicron spike variant XBB with Bn03

• PDB DOI: https://doi.org/10.2210/pdb8I4E/pdb
• EM Map EMD-35170: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2023-01-19 Released: 2023-12-27 
• Deposition Author(s): Hao, A.H., Zhang, X., Chen, Z.G., Sun, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.98 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Defining a highly conserved cryptic epitope for antibody recognition of SARS-CoV-2 variants.

Hao, A., Song, W., Li, C., Zhang, X., Tu, C., Wang, X., Wang, P., Wu, Y., Ying, T., Sun, L.

(2023) Signal Transduct Target Ther 8: 269-269

• PubMed: 37422451 
• DOI: https://doi.org/10.1038/s41392-023-01534-0
• Primary Citation of Related Structures:  
  8I4E, 8I4F, 8I4G, 8I4H

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Organizational Affiliation: 

MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Engineering Research Center for Synthetic Immunology, Shanghai Fifth People's Hospital, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 170.74 kDa 
• Atom Count: 5,824 
• Modelled Residue Count: 738 
• Deposited Residue Count: 1,553 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	1,295	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 34  Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Bn03	B [auth C]	258	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.98 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-12-27 
Deposition Author(s): Hao, A.H., Zhang, X., Chen, Z.G., Sun, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81900729

Revision History  

• Version 1.0: 2023-12-27
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary