8W50

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

• PDB DOI: https://doi.org/10.2210/pdb8W50/pdb

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


• Deposited: 2023-08-25 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: 2.67 Å
• R-Value Free: 0.248 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

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.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 371.96 kDa 
• Atom Count: 20,918 
• Modelled Residue Count: 2,745 
• Deposited Residue Count: 3,224 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase 2-alpha	A, B, C, D	806	Homo sapiens	Mutation(s): 0  Gene Names: TOP2A, TOP2 EC: 5.99.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P11388 (Homo sapiens) Explore P11388  Go to UniProtKB:  P11388
PHAROS:  P11388 GTEx:  ENSG00000131747

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 0.248 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 266.104	α = 90
b = 266.104	β = 90
c = 172.812	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
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