Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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: 37.90 kDa 
• Atom Count: 1955 
• Modelled Residue Count: 245 
• Deposited Residue Count: 329 
• Unique protein chains: 1

1V0D

Crystal Structure of Caspase-activated DNase (CAD)

• PDB DOI: 10.2210/pdb1V0D/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• 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.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.246 
• R-Value Work: 0.218 
• R-Value Observed: 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 
• DOI: 10.1016/s1097-2765(04)00258-8
• Primary Citation of 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA FRAGMENTATION FACTOR 40 KDA SUBUNIT	A	329	Mus musculus	Mutation(s): 0  Gene Names: Dffb, Cad EC: 3
UniProt & NIH Common Fund Data Resources
Find proteins for O54788 (Mus musculus) Explore O54788  Go to UniProtKB:  O54788
IMPC:  MGI:1196287

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.246 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.189	α = 90
b = 110.189	β = 90
c = 73.982	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance