8Z6R | pdb_00008z6r

Structure of XBB.1.16 S trimer with 3 down-RBDs complex with antibody CYFN1006-1.

• PDB DOI: https://doi.org/10.2210/pdb8Z6R/pdb
• EM Map EMD-39802: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4, synthetic construct, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-04-19 Released: 2025-01-29 
• Deposition Author(s): Wang, Y.J., Sun, L.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of XBB.1.16 S trimer with 3 down-RBDs complex with antibody CYFN1006-1.

Wang, Y.J., Sun, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 647.74 kDa 
• Atom Count: 33,554 
• Modeled Residue Count: 4,329 
• Deposited Residue Count: 5,895 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein,Fibritin,Spike glycoprotein,Fibritin,Spike glycoprotein,Fibritin,Expression Tag	A, H [auth B], I [auth C]	1,299	Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4, synthetic construct This entity is chimeric	Mutation(s): 39  Gene Names: S, 2, wac
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104  Go to UniProtKB:  P10104
UniProt Groups	P0DTC2P10104

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYFN1006-1 light chain	B [auth D], D [auth F], F [auth H]	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CYFN1006-1 heavy chain	C [auth E], E [auth G], G [auth I]	451	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.87 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: 2025-01-29 
Deposition Author(s): Wang, Y.J., Sun, L.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release
  
• Version 1.1: 2025-07-23
  Changes: Data collection