Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer -A2B 

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

Macromolecule Content

• Total Structure Weight: 150690.41 
• Atom Count: 8470 
• Residue Count: 1302 
• Unique protein chains: 2

2A5Y

Structure of a CED-4/CED-9 complex

• DOI: 10.2210/pdb2A5Y/pdb

• Classification: APOPTOSIS
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): 3 


• Deposited: 2005-07-01 Released: 2005-10-11 
• Deposition Author(s): Yan, N., Liu, Q., Hao, Q., Gu, L., Shi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.277 
• R-Value Work: 0.249 

Literature

Structure of the CED-4-CED-9 complex provides insights into programmed cell death in Caenorhabditis elegans.

Yan, N., Chai, J., Lee, E.S., Gu, L., Liu, Q., He, J., Wu, J.W., Kokel, D., Li, H., Hao, Q., Xue, D., Shi, Y.

(2005) Nature 437: 831-837

• PubMed: 16208361 
• DOI: 10.1038/nature04002


• PubMed Abstract: 
  

Interplay among four genes--egl-1, ced-9, ced-4 and ced-3--controls the onset of programmed cell death in the nematode Caenorhabditis elegans. Activation of the cell-killing protease CED-3 requires CED-4. However, CED-4 is constitutively inhibited by CED-9 until its release by EGL-1. Here we report the crystal structure of the CED-4-CED-9 complex at 2.6 A resolution, and a complete reconstitution of the CED-3 activation pathway using homogeneous proteins of CED-4, CED-9 and EGL-1. One molecule of CED-9 binds to an asymmetric dimer of CED-4, but specifically recognizes only one of the two CED-4 molecules. This specific interaction prevents CED-4 from activating CED-3. EGL-1 binding induces pronounced conformational changes in CED-9 that result in the dissociation of the CED-4 dimer from CED-9. The released CED-4 dimer further dimerizes to form a tetramer, which facilitates the autoactivation of CED-3. Together, our studies provide important insights into the regulation of cell death activation in C. elegans.

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Organizational Affiliation: 

Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey 08544, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Apoptosis regulator ced-9	A	204	Caenorhabditis elegans	Mutation(s): 3  Gene Names: ced-9
Find proteins for P41958 (Caenorhabditis elegans) Go to UniProtKB:  P41958

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
ced-4	B, C	549	Caenorhabditis elegans	Mutation(s): 0  Gene Names: ced-4
Find proteins for P30429 (Caenorhabditis elegans) Go to UniProtKB:  P30429

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ATP	B, C	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	B, C	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.6 Å
• R-Value Free: 0.277 
• R-Value Work: 0.249 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 128.898	α = 90.00
b = 128.898	β = 90.00
c = 209.928	γ = 90.00

Software Package:

Software Name	Purpose
CNS	refinement
SOLVE	phasing
HKL-2000	data reduction
SCALEPACK	data scaling
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-07-01 
• Released Date: 2005-10-11 
• Deposition Author(s): Yan, N., Liu, Q., Hao, Q., Gu, L., Shi, Y.

Revision History 

• Version 1.0: 2005-10-11
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance