1A36 | pdb_00001a36

TOPOISOMERASE I/DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1A36/pdb
• NAKB: 1A36

• Classification: ISOMERASE/DNA
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 1998-01-29 Released: 1998-08-12 
• Deposition Author(s): Stewart, L., Redinbo, M.R., Qiu, X., Champoux, J.J., Hol, W.G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.312 (Depositor) 
• R-Value Work: 
  0.224 (Depositor) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

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: 9488652 
• DOI: https://doi.org/10.1126/science.279.5356.1534
• Primary Citation Related Structures: 
  1A36


• 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 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."

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Organizational Affiliation: 
• Biomolecular Structure Center and Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA 98195-7742, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 83.52 kDa 
• Atom Count: 5,285 
• Modeled Residue Count: 588 
• Deposited Residue Count: 635 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TOPOISOMERASE I	C [auth A]	591	Homo sapiens	Mutation(s): 1  EC: 5.99.1.2 (PDB Primary Data), 5.6.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P11387 (Homo sapiens) Explore P11387  Go to UniProtKB:  P11387
PHAROS:  P11387 GTEx:  ENSG00000198900

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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')	A [auth B]	22	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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')	B [auth C]	22	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.312 (Depositor) 
• R-Value Work:  0.224 (Depositor) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.5	α = 90
b = 118.4	β = 101.2
c = 71.5	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: 1998-08-12 
Deposition Author(s): Stewart, L., Redinbo, M.R., Qiu, X., Champoux, J.J., Hol, W.G.J.

Revision History  

• Version 1.0: 1998-08-12
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references
• Version 1.4: 2024-02-07
  Changes: Data collection
• Version 1.5: 2024-04-03
  Changes: Refinement description