Human Topo IIa ATPase/AMP-PNP

Experimental Data Snapshot

  • Resolution: 1.87 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

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Nucleotide-dependent Domain Movement in the ATPase Domain of a Human Type IIA DNA Topoisomerase.

Wei, H.Ruthenburg, A.J.Bechis, S.K.Verdine, G.L.

(2005) J Biol Chem 280: 37041-37047

  • DOI: https://doi.org/10.1074/jbc.M506520200
  • Primary Citation of Related Structures:  
    1ZXM, 1ZXN

  • PubMed Abstract: 

    Type IIA DNA topoisomerases play multiple essential roles in the management of higher-order DNA structure, including modulation of topological state, chromosome segregation, and chromatin condensation. These diverse physiologic functions are all accomplished through a common molecular mechanism, wherein the protein catalyzes transient cleavage of a DNA duplex (the G-segment) to yield a double-stranded gap through which another duplex (the T-segment) is passed. The overall process is orchestrated by the opening and closing of molecular "gates" in the topoisomerase structure, which is regulated by ATP binding, hydrolysis, and release of ADP and inorganic phosphate. Here we present two crystal structures of the ATPase domain of human DNA topoisomerase IIalpha in different nucleotide-bound states. Comparison of these structures revealed rigid-body movement of the structural modules within the ATPase domain, suggestive of the motions of a molecular gate.

  • Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase II, alpha isozyme
A, B
400Homo sapiensMutation(s): 0 
Gene Names: TOP2ATOP2
EC: (PDB Primary Data), (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11388 (Homo sapiens)
Explore P11388 
Go to UniProtKB:  P11388
PHAROS:  P11388
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11388
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.87 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.772α = 90
b = 75.285β = 90
c = 164.887γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance