1BJT | pdb_00001bjt

TOPOISOMERASE II RESIDUES 409-1201

• PDB DOI: https://doi.org/10.2210/pdb1BJT/pdb

• Classification: TOPOISOMERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 1998-06-29 Released: 1999-05-04 
• Deposition Author(s): Fass, D., Bogden, C.E., Berger, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.269 (Depositor) 
• R-Value Work: 
  0.227 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Literature

Quaternary changes in topoisomerase II may direct orthogonal movement of two DNA strands.

Fass, D., Bogden, C.E., Berger, J.M.

(1999) Nat Struct Biol 6: 322-326

• PubMed: 10201398 
• DOI: https://doi.org/10.1038/7556
• Primary Citation of Related Structures:  
  1BJT


• PubMed Abstract: 
  

  Type II DNA topoisomerases mediate the passage of one DNA duplex through a transient break in another, an event essential for chromosome segregation and cell viability. The active sites of the type II topoisomerase dimer associate covalently with the DNA break-points and must separate by at least the width of the second DNA duplex to accommodate transport. A new structure of the Saccharomyces cerevisiae topoisomerase II DNA-binding and cleavage core suggests that in addition to conformational changes in the DNA-opening platform, a dramatic reorganization of accessory domains may occur during catalysis. These conformational differences have implications for both the DNA-breaking and duplex-transport events in the topo II reaction mechanism, suggest a mechanism by which two distinct drug-resistance loci interact, and illustrate the scope of structural changes in the cycling of molecular machines.

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Organizational Affiliation: 

Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02140, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 91.81 kDa 
• Atom Count: 5,815 
• Modelled Residue Count: 679 
• Deposited Residue Count: 793 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TOPOISOMERASE II	A	793	Saccharomyces cerevisiae	Mutation(s): 0  EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P06786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06786  Go to UniProtKB:  P06786

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.269 (Depositor) 
• R-Value Work:  0.227 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.4	α = 90
b = 145.7	β = 90
c = 161.3	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-04 
Deposition Author(s): Fass, D., Bogden, C.E., Berger, J.M.

Revision History  

• Version 1.0: 1999-05-04
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Other