3QX3

Human topoisomerase IIbeta in complex with DNA and etoposide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.162 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of type II topoisomerase inhibition by the anticancer drug etoposide

Wu, C.C.Li, T.K.Farh, L.Lin, L.Y.Lin, T.S.Yu, Y.J.Yen, T.J.Chiang, C.W.Chan, N.L.

(2011) Science 333: 459-462

  • DOI: 10.1126/science.1204117

  • PubMed Abstract: 
  • Type II topoisomerases (TOP2s) resolve the topological problems of DNA by transiently cleaving both strands of a DNA duplex to form a cleavage complex through which another DNA segment can be transported. Several widely prescribed anticancer drugs in ...

    Type II topoisomerases (TOP2s) resolve the topological problems of DNA by transiently cleaving both strands of a DNA duplex to form a cleavage complex through which another DNA segment can be transported. Several widely prescribed anticancer drugs increase the population of TOP2 cleavage complex, which leads to TOP2-mediated chromosome DNA breakage and death of cancer cells. We present the crystal structure of a large fragment of human TOP2β complexed to DNA and to the anticancer drug etoposide to reveal structural details of drug-induced stabilization of a cleavage complex. The interplay between the protein, the DNA, and the drug explains the structure-activity relations of etoposide derivatives and the molecular basis of drug-resistant mutations. The analysis of protein-drug interactions provides information applicable for developing an isoform-specific TOP2-targeting strategy.


    Organizational Affiliation

    Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei City 100, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 2-beta
A, B
803Homo sapiensGene Names: TOP2B
EC: 5.99.1.3
Find proteins for Q02880 (Homo sapiens)
Go to Gene View: TOP2B
Go to UniProtKB:  Q02880
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')C,E8N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')D,F12N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EVP
Query on EVP

Download SDF File 
Download CCD File 
A, D
(5S,5aR,8aR,9R)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside
Etoposide; VP-16
C29 H32 O13
VJJPUSNTGOMMGY-MRVIYFEKSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EVPEC50: >70000 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.162 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.149α = 90.00
b = 176.801β = 111.58
c = 94.067γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
Blu-Icedata collection
PHENIXrefinement
HKL-2000data reduction
PHENIXmodel building
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-01-25
    Type: Database references