8YLU

structure of phage T6 topoisomerase II central domain bound with DNA

• PDB DOI: https://doi.org/10.2210/pdb8YLU/pdb
• EM Map EMD-39391: EMDB EMDataResource
• NAKB: 8YLU

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


• Deposited: 2024-03-06 Released: 2024-09-25 
• 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: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

structure of phage T6 topoisomerase II central domain bound with DNA

Chen, Y.T., Xin, Y.H.

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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 255.9 kDa 
• Atom Count: 11,441 
• Modelled Residue Count: 1,352 
• Deposited Residue Count: 2,170 
• 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	Salmonella phage Chi	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(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))	E	22	DNA molecule

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*AP*TP*AP*TP*GP*TP*GP*TP*AP*TP*AP*TP*AP*TP*AP*CP*AP*CP*AP*CP*A)-3')	F	22	DNA molecule

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 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.

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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