Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 71.32 kDa 
• Atom Count: 4997 
• Residue Count: 591 
• Unique protein chains: 1

3CG7

Crystal structure of cell-death related nuclease 4 (CRN-4)

• DOI: 10.2210/pdb3CG7/pdb

• Classification: HYDROLASE, APOPTOSIS
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-03-05 Released: 2008-12-30 
• Deposition Author(s): Hsiao, Y.-Y., Yuan, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.247 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 

Literature

Crystal structure of CRN-4: implications for domain function in apoptotic DNA degradation

Hsiao, Y.-Y., Nakagawa, A., Shi, Z., Mitani, S., Xue, D., Yuan, H.S.

(2009) Mol Cell Biol 29: 448-457

• PubMed: 18981218 
• DOI: 10.1128/MCB.01006-08
• Primary Citation of Related Structures:  
  3CG7, 3CM5, 3CM6


• PubMed Abstract: 
  

Cell death related nuclease 4 (CRN-4) is one of the apoptotic nucleases involved in DNA degradation in Caenorhabditis elegans. To understand how CRN-4 is involved in apoptotic DNA fragmentation, we analyzed CRN-4's biochemical properties, in vivo cell functions, and the crystal structures of CRN-4 in apo-form, Mn(2+)-bound active form, and Er(3+)-bound inactive form. CRN-4 is a dimeric nuclease with the optimal enzyme activity in cleaving double-stranded DNA in apoptotic salt conditions. Both mutational studies and the structures of the Mn(2+)-bound CRN-4 revealed the geometry of the functional nuclease active site in the N-terminal DEDDh domain. The C-terminal domain, termed the Zn-domain, contains basic surface residues ideal for nucleic acid recognition and is involved in DNA binding, as confirmed by deletion assays. Cell death analysis in C. elegans further demonstrated that both the nuclease active site and the Zn-domain are required for crn-4's function in apoptosis. Combining all of the data, we suggest a structural model where chromosomal DNA is bound at the Zn-domain and cleaved at the DEDDh nuclease domain in CRN-4 when the cell is undergoing apoptosis.

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Organizational Affiliation: 

Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell death-related nuclease 4	A, B	308	Caenorhabditis elegans	Mutation(s): 0  Gene Names: crn-4, AH9.2 EC: 3.1
Find proteins for Q10905 (Caenorhabditis elegans) Explore Q10905  Go to UniProtKB:  Q10905

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.247 
• R-Value Work: 0.206 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.474	α = 90
b = 165.379	β = 90
c = 64.263	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-03-05 
• Released Date: 2008-12-30 
Deposition Author(s): Hsiao, Y.-Y., Yuan, H.S.

Revision History 

• Version 1.0: 2008-12-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance