1A35 | pdb_00001a35

HUMAN TOPOISOMERASE I/DNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1A35/pdb
• NAKB: 1A35

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


• Deposited: 1998-01-29 Released: 1998-08-28 
• Deposition Author(s): Redinbo, M.R., Stewart, L., Kuhn, P., Champoux, J.J., Hol, W.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.308 (Depositor) 
• R-Value Work: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA.

Redinbo, M.R., Stewart, L., Kuhn, P., Champoux, J.J., Hol, W.G.

(1998) Science 279: 1504-1513

• PubMed: 9488644 
• DOI: https://doi.org/10.1126/science.279.5356.1504
• Primary Citation Related Structures: 
  1A31, 1A35


• PubMed Abstract: 
  

  Topoisomerases I promote the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. The crystal structures at 2.1 and 2.5 angstrom resolution of reconstituted human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps" around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin is proposed on the basis of chemical and biochemical information combined with these three-dimensional structures of topoisomerase I-DNA complexes.

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Organizational Affiliation: 
• Biomolecular Structure Center and Department of Biological Structure, Box 357742, School of Medicine, University of Washington, Seattle, WA 98195, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 84.04 kDa 
• Atom Count: 4,947 
• Modeled Residue Count: 518 
• Deposited Residue Count: 635 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (DNA 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*AP*(BRU)P*(BRU)P*TP*TP*T)-3')	A [auth C]	22	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*AP*AP*TP*+UP*+UP*+UP*+UP*CP*+UP*AP*AP*GP*TP*CP*TP*TP*TP*+ UP*T)-3')	B [auth D]	22	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.308 (Depositor) 
• R-Value Work:  0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.8	α = 90
b = 66.3	β = 98.4
c = 71.8	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: 1998-08-28 
Deposition Author(s): Redinbo, M.R., Stewart, L., Kuhn, P., Champoux, J.J., Hol, W.G.

Revision History  

• Version 1.0: 1998-08-28
  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, Derived calculations
• Version 1.4: 2024-02-07
  Changes: Data collection
• Version 1.5: 2024-04-03
  Changes: Refinement description