9KT3 | pdb_00009kt3

Structure of EG.5.1 S trimer with 2 down-RBDs complex with antibody CYFN1006-2.

• PDB DOI: https://doi.org/10.2210/pdb9KT3/pdb
• EM Map EMD-62556: EMDB EMDataResource

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


• Deposited: 2024-12-01 Released: 2025-01-29 
• Deposition Author(s): Wang, Y.J., Sun, L.
• Funding Organization(s): Not funded

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.63 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of EG.5.1 S trimer with 2 down-RBDs complex with antibody CYFN1006-2.

Wang, Y.J., Sun, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 567.63 kDa 
• Atom Count: 34,950 
• Modeled Residue Count: 4,524 
• Deposited Residue Count: 5,184 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein,Fibritin,Expression Tag	A, D [auth B], I [auth C]	1,295	Severe acute respiratory syndrome coronavirus 2, Tequatrovirus T4, synthetic construct This entity is chimeric	Mutation(s): 42  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
CYFN1006-2 light chain	B [auth K], E [auth J], G [auth L]	215	Tequatrovirus T4	Mutation(s): 0  Gene Names: wac

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CYFN1006-2 heavy chain	C [auth H], F [auth G], H [auth I]	218	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.63 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.17.1_3660

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-29 
Deposition Author(s): Wang, Y.J., Sun, L.

---

Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-01-29
  Type: Initial release