Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 92.38 kDa 
• Atom Count: 6521 
• Modelled Residue Count: 751 
• Deposited Residue Count: 800 
• Unique protein chains: 1

1ZXM

Human Topo IIa ATPase/AMP-PNP

• PDB DOI: 10.2210/pdb1ZXM/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-06-08 Released: 2005-08-23 
• Deposition Author(s): Wei, H., Ruthenburg, A.J., Bechis, S.K., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 0.243 
• R-Value Work: 0.220 
• R-Value Observed: 0.220 

Literature

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

• PubMed: 16100112 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA topoisomerase II, alpha isozyme	A, B	400	Homo sapiens	Mutation(s): 0  Gene Names: TOP2A, TOP2 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11388 (Homo sapiens) Explore P11388  Go to UniProtKB:  P11388
PHAROS:  P11388

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP	D [auth A], F [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 70.772	α = 90
b = 75.285	β = 90
c = 164.887	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-08 
• Released Date: 2005-08-23 
Deposition Author(s): Wei, H., Ruthenburg, A.J., Bechis, S.K., Verdine, G.L.

Revision History  

• 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