Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 37897.58 
• Atom Count: 1939 
• Residue Count: 329 
• Unique protein chains: 1

1V0D

Crystal Structure of Caspase-activated DNase (CAD)

• DOI: 10.2210/pdb1V0D/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2004-03-26 Released: 2004-05-21 
• Deposition Author(s): Woo, E.-J., Kim, Y.-G., Kim, M.-S., Han, W.-D., Shin, S., Oh, B.-H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.246 
• R-Value Work: 0.218 

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

• PubMed: 15149602 


• 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.

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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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT	A	329	Mus musculus	Mutation(s): 0  Gene Names: Dffb (Cad) EC: 3.-.-.-
Find proteins for O54788 (Mus musculus) Go to UniProtKB:  O54788

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
PB	A	LEAD (II) ION Pb RVPVRDXYQKGNMQ-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.246 
• R-Value Work: 0.218 
• Space Group: P 6₄

Unit Cell:

Length (Å)	Angle (°)
a = 110.189	α = 90.00
b = 110.189	β = 90.00
c = 73.982	γ = 120.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-26 
• Released Date: 2004-05-21 
• Deposition Author(s): Woo, E.-J., Kim, Y.-G., Kim, M.-S., Han, W.-D., Shin, S., Oh, B.-H.

Revision History 

• Version 1.0: 2004-05-21
  Type: Initial release
• Version 1.1: 2011-05-07
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance