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 
  • R-Value Observed: 0.224 

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
  • Primary Citation of Related Structures:  
    5ZEN, 5ZQF, 5ZRF

  • 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 to change the DNA topology ...

    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

    Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan. nlchan@ntu.edu.tw.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 2-betaA803Homo sapiensMutation(s): 0 
Gene Names: TOP2B
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q02880 (Homo sapiens)
Explore Q02880 
Go to UniProtKB:  Q02880
PHAROS:  Q02880
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02880
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3')B8synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*AP*GP*CP*TP*CP*GP*GP*CP*T)-3')C9synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth 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 
  • R-Value Observed: 0.224 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.76α = 90
b = 95.76β = 90
c = 231.055γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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