5ZEN

Crystal structure of human topoisomerase II beta in complex with DNA: a new quaternary conformation showing opening of the protein-linked DNA-gate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into the gating of DNA passage by the topoisomerase II DNA-gate.

Chen, S.F.Huang, N.L.Lin, J.H.Wu, C.C.Wang, Y.R.Yu, Y.J.Gilson, M.K.Chan, N.L.

(2018) Nat Commun 9: 3085-3085

  • DOI: 10.1038/s41467-018-05406-y

  • PubMed Abstract: 
  • Type IIA topoisomerases (Top2s) manipulate the handedness of DNA crossovers by introducing a transient and protein-linked double-strand break in one DNA duplex, termed the DNA-gate, whose opening allows another DNA segment to be transported through t ...

    Type IIA topoisomerases (Top2s) manipulate the handedness of DNA crossovers by introducing a transient and protein-linked double-strand break in one DNA duplex, termed the DNA-gate, whose opening allows another DNA segment to be transported through to change the DNA topology. Despite the central importance of this gate-opening event to Top2 function, the DNA-gate in all reported structures of Top2-DNA complexes is in the closed state. Here we present the crystal structure of a human Top2 DNA-gate in an open conformation, which not only reveals structural characteristics of its DNA-conducting path, but also uncovers unexpected yet functionally significant conformational changes associated with gate-opening. This structure further implicates Top2's preference for a left-handed DNA braid and allows the construction of a model representing the initial entry of another DNA duplex into the DNA-gate. Steered molecular dynamics calculations suggests the Top2-catalyzed DNA passage may be achieved by a rocker-switch-type movement of the DNA-gate.


    Organizational Affiliation

    Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA topoisomerase 2-beta
A
803Homo sapiensMutation(s): 0 
Gene 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')B8synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')C9synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 95.760α = 90.00
b = 95.760β = 90.00
c = 231.055γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2018-08-15
    Type: Data collection, Database references