8YON

structure of phage T6 full-length topoisomerase II bound with DNA

• PDB DOI: https://doi.org/10.2210/pdb8YON/pdb
• EM Map EMD-39454: EMDB EMDataResource
• NAKB: 8YON

• Classification: ISOMERASE
• Organism(s): Escherichia phage T4, Enterobacteria phage T6, DNA molecule
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-13 Released: 2024-09-25 
• Deposition Author(s): Chen, Y.T., Xin, Y.H., Xian, R.Q.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

structure of phage T6 full-length topoisomerase II bound with DNA

Chen, Y.T., Xin, Y.H., Xian, R.Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 275.41 kDa 
• Atom Count: 18,822 
• Modelled Residue Count: 2,192 
• Deposited Residue Count: 2,230 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase medium subunit	A, B	452	Escherichia phage T4	Mutation(s): 0  Gene Names: 52 EC: 5.6.2.2
UniProt
Find proteins for P07065 (Enterobacteria phage T4) Explore P07065  Go to UniProtKB:  P07065

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase (ATP-hydrolyzing)	C, D	611	Enterobacteria phage T6	Mutation(s): 0  Gene Names: EcT6_00003 EC: 5.6.2.2
UniProt
Find proteins for A0A346FJ89 (Enterobacteria phage T6) Explore A0A346FJ89  Go to UniProtKB:  A0A346FJ89

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (50-MER)	E	52	DNA molecule

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (50-MER)	F	52	DNA molecule

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	G [auth C], H [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.73 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Chen, Y.T., Xin, Y.H., Xian, R.Q.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	--

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release