9JOR | pdb_00009jor

structure of phage T4 topoisomerase II central domain bound with DNA

• PDB DOI: https://doi.org/10.2210/pdb9JOR/pdb
• EM Map EMD-61683: EMDB EMDataResource
• NAKB: 9JOR

• Classification: ISOMERASE
• Organism(s): Tequatrovirus T4, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-25 Released: 2025-10-22 
• Deposition Author(s): Chen, Y.T., Xin, Y.H.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.09 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

structure of phage T4 topoisomerase II central domain bound with DNA

Chen, Y.T., Xin, Y.H., Xian, R.Q.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 273.76 kDa 
• Atom Count: 12,697 
• Modeled Residue Count: 1,500 
• Deposited Residue Count: 2,316 
• 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 [auth C], C [auth D]	452	Tequatrovirus 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 large subunit,DNA topoisomerase small subunit	B [auth A], D [auth B]	682	Tequatrovirus T4	Mutation(s): 0  Gene Names: 39, 60 EC: 5.6.2.2
UniProt
Find proteins for P09176 (Enterobacteria phage T4) Explore P09176  Go to UniProtKB:  P09176
Find proteins for P23992 (Enterobacteria phage T4) Explore P23992  Go to UniProtKB:  P23992
UniProt Groups	P23992P09176

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*GP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*TP*AP*TP*AP*TP*A)-3')	E	24	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*CP*AP*T)-3')	F	24	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.09 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Chen, Y.T., Xin, Y.H.

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

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release