8KE7

Crystal structure of DNA binding and cleavage core of human topoisomerase 2-beta in a DNA binding-competent conformation

• PDB DOI: https://doi.org/10.2210/pdb8KE7/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-11 Released: 2024-07-24 
• Deposition Author(s): Chan, N.L., Liu, K.T., Chen, S.F.
• Funding Organization(s): National Science Council (NSC, Taiwan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.238 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Starting Model: experimental

Literature

Structural Basis for the Assembly of Type IIA Topoisomerase DNA Cleavage/Religation Center

Chan, N.L., Liu, K.T., Chen, S.F.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 184.39 kDa 
• Atom Count: 11,666 
• Modelled Residue Count: 1,457 
• Deposited Residue Count: 1,606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2-beta	A, B	803	Homo sapiens	Mutation(s): 0  Gene Names: TOP2B EC: 5.99.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q02880 (Homo sapiens) Explore Q02880  Go to UniProtKB:  Q02880
PHAROS:  Q02880 GTEx:  ENSG00000077097

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.238 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.719	α = 90
b = 113.708	β = 90
c = 209.267	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Chan, N.L., Liu, K.T., Chen, S.F.

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Funding Organization	Location	Grant Number
National Science Council (NSC, Taiwan)	Taiwan	--

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release