5ZRF

Crystal structure of human topoisomerase II beta in complex with 5-iodouridine-containing-DNA and etoposide in space group p21

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 

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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-betaA, B803Homo 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')C, E8synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA/RNA (5'-R(P*(IU))-D(P*GP*CP*AP*GP*C)-R(P*(IU))-D(P*CP*GP*GP*C)-R(P*(IU))-3')D, F12synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EVP
Query on EVP
Download Ideal Coordinates CCD File 
K [auth D],
M [auth F]		(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
C29 H32 O13
VJJPUSNTGOMMGY-MRVIYFEKSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth B],
J [auth B],
L [auth D],
G [auth A],
H [auth A],
I [auth B],
J [auth B],
L [auth D],
N [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
EVP BindingDB:  5ZRF IC50: min: 70, max: 790 (nM) from 2 assay(s)
EC50: 7.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.147α = 90
b = 176.27β = 111.44
c = 94.331γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
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: 2019-02-20
    Changes: Data collection, Database references