1V0D | pdb_00001v0d

Crystal Structure of Caspase-activated DNase (CAD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.246 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.218 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural Mechanism for Inactivation and Activation of Cad/Dff40 in the Apoptotic Pathway

Woo, E.-J.Kim, Y.-G.Kim, M.-S.Han, W.-D.Shin, S.Robinson, H.Park, S.-Y.Oh, B.-H.

(2004) Mol Cell 14: 531

  • DOI: https://doi.org/10.1016/s1097-2765(04)00258-8
  • Primary Citation Related Structures: 
    1V0D

  • PubMed Abstract: 

    CAD/DFF40 is responsible for the degradation of chromosomal DNA into nucleosomal fragments and subsequent chromatin condensation during apoptosis. It exists as an inactive complex with its inhibitor ICAD/DFF45 in proliferating cells but becomes activated upon cleavage of ICAD/DFF45 into three domains by caspases in dying cells. The molecular mechanism underlying the control and activation of CAD/DFF40 was unknown. Here, the crystal structure of activated CAD/DFF40 reveals that it is a pair of molecular scissors with a deep active-site crevice that appears ideal for distinguishing internucleosomal DNA from nucleosomal DNA. Ensuing studies show that ICAD/DFF45 sequesters the nonfunctional CAD/DFF40 monomer and is also able to disassemble the functional CAD/DFF40 dimer. This capacity requires the involvement of the middle domain of ICAD/DFF45, which by itself cannot remain bound to CAD/DFF40 due to low binding affinity for the enzyme. Thus, the consequence of the caspase-cleavage of ICAD/DFF45 is a self-assembly of CAD/DFF40 into the active dimer.


  • Organizational Affiliation
    • Division of Molecular and Life Sciences, Department of Life Sciences and Center for Biomolecular Recognition, Pohang University of Science and Technology, Pohang, Kyungbuk 790-784, South Korea.

Macromolecule Content 

  • Total Structure Weight: 37.9 kDa 
  • Atom Count: 1,955 
  • Modeled Residue Count: 245 
  • Deposited Residue Count: 329 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT329Mus musculusMutation(s): 0 
EC: 3
UniProt & NIH Common Fund Data Resources
Find proteins for O54788 (Mus musculus)
Explore O54788 
Go to UniProtKB:  O54788
IMPC:  MGI:1196287
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO54788
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.246 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.218 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.189α = 90
b = 110.189β = 90
c = 73.982γ = 120
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-21
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other