8YWE | pdb_00008ywe

Local refinement of SARS-CoV-2 Omicron BA.2.86 S complexed with Abs G7-Fc

• PDB DOI: https://doi.org/10.2210/pdb8YWE/pdb
• EM Map EMD-39630: 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: 2024-03-31 Released: 2025-04-02 
• Deposition Author(s): Ma, Y., Liu, Q., Rehati, P., Zhang, Z.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.69 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Impact of scFv Sequence and Position on the Functionality of Bispecific Antibodies against Omicron Variants EG.5 and BA.2.86

Ma, Y., Liu, Q., Rehati, P., Zhang, Z., Zhao, J., Wu, F., Sun, L., Huang, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 79.35 kDa 
• Atom Count: 5,271 
• Modeled Residue Count: 681 
• Deposited Residue Count: 733 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike protein S1	A	222	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 18  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
GW01 scFv	B	251	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
7F3 scFv	C	260	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.69 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-04-02 
Deposition Author(s): Ma, Y., Liu, Q., Rehati, P., Zhang, Z.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-04-02
  Type: Initial release
  
• Version 1.1: 2025-07-16
  Changes: Data collection