1A36

TOPOISOMERASE I/DNA COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A model for the mechanism of human topoisomerase I.

Stewart, L.Redinbo, M.R.Qiu, X.Hol, W.G.Champoux, J.J.

(1998) Science 279: 1534-1541


  • PubMed Abstract: 
  • The three-dimensional structure of a 70-kilodalton amino terminally truncated form of human topoisomerase I in complex with a 22-base pair duplex oligonucleotide, determined to a resolution of 2.8 angstroms, reveals all of the structural elements of ...

    The three-dimensional structure of a 70-kilodalton amino terminally truncated form of human topoisomerase I in complex with a 22-base pair duplex oligonucleotide, determined to a resolution of 2.8 angstroms, reveals all of the structural elements of the enzyme that contact DNA. The linker region that connects the central core of the enzyme to the carboxyl-terminal domain assumes a coiled-coil configuration and protrudes away from the remainder of the enzyme. The positively charged DNA-proximal surface of the linker makes only a few contacts with the DNA downstream of the cleavage site. In combination with the crystal structures of the reconstituted human topoisomerase I before and after DNA cleavage, this information suggests which amino acid residues are involved in catalyzing phosphodiester bond breakage and religation. The structures also lead to the proposal that the topoisomerization step occurs by a mechanism termed "controlled rotation."


    Organizational Affiliation

    Biomolecular Structure Center and Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA 98195-7742, USA. emerald_biostructures@rocketmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
TOPOISOMERASE I
A
591Homo sapiensGene Names: TOP1
EC: 5.99.1.2
Find proteins for P11387 (Homo sapiens)
Go to Gene View: TOP1
Go to UniProtKB:  P11387
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*AP*AP*GP*AP*CP*TP*TP*AP*GP*AP*AP*AP*AP*A P*TP*TP*TP*TP*T)- 3')B22N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*AP*AP*TP*TP*TP*TP*TP*CP*TP*AP*AP*GP*TP*C P*TP*TP*TP*TP*T)- 3')C22N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.500α = 90.00
b = 118.400β = 101.20
c = 71.500γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORphasing
X-PLORmodel building
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-12
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance