9JNK | pdb_00009jnk

Bacteriophage T4 topoisomerse II bound with a T-segment DNA

• PDB DOI: https://doi.org/10.2210/pdb9JNK/pdb
• EM Map EMD-61621: EMDB EMDataResource
• NAKB: 9JNK

• Classification: ISOMERASE/DNA
• Organism(s): Tequatrovirus T4, DNA molecule
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-23 Released: 2025-10-01 
• Deposition Author(s): Xin, Y.H., Chen, Y.T.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural and functional insights into the T-even type bacteriophage topoisomerase II

Xin, Y.H., Chen, Y.T.

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: 274.3 kDa 
• Atom Count: 12,539 
• Modeled Residue Count: 1,480 
• Deposited Residue Count: 2,318 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase large subunit,DNA topoisomerase small subunit	A, C [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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase medium subunit	B [auth C], 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: 3
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	E	25	DNA molecule

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	F	25	DNA molecule

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.03 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Xin, Y.H., Chen, Y.T.

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

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release