Biological Assembly 1  

 3D View: Structure | Electron Density

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: 69.47 kDa 
• Atom Count: 3821 
• Residue Count: 479 
• Unique protein chains: 1

4M9R

Crystal structure of CED-3

• DOI: 10.2210/pdb4M9R/pdb

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


• Deposited: 2013-08-15 Released: 2013-10-09 
• Deposition Author(s): Xu, Y., Jeffrey, P.D., Shi, Y.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.260 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Literature

Mechanistic insights into CED-4-mediated activation of CED-3

Huang, W., Jiang, T., Choi, W., Qi, S., Pang, Y., Hu, Q., Xu, Y., Gong, X., Jeffrey, P.D., Wang, J., Shi, Y.G.

(2013) Genes Dev 27: 2039-2048

• PubMed: 24065769 
• DOI: 10.1101/gad.224428.113
• Primary Citation of Related Structures:  
  4M9X, 4M9Y, 4M9Z, 4M9R, 4M9S


• PubMed Abstract: 
  

Programmed cell death in Caenorhabditis elegans requires activation of the caspase CED-3, which strictly depends on CED-4. CED-4 forms an octameric apoptosome, which binds the CED-3 zymogen and facilitates its autocatalytic maturation. Despite recent advances, major questions remain unanswered. Importantly, how CED-4 recognizes CED-3 and how such binding facilitates CED-3 activation remain completely unknown. Here we demonstrate that the L2' loop of CED-3 directly binds CED-4 and plays a major role in the formation of an active CED-4-CED-3 holoenzyme. The crystal structure of the CED-4 apoptosome bound to the L2' loop fragment of CED-3, determined at 3.2 Å resolution, reveals specific interactions between a stretch of five hydrophobic amino acids from CED-3 and a shallow surface pocket within the hutch of the funnel-shaped CED-4 apoptosome. Structure-guided biochemical analysis confirms the functional importance of the observed CED-4-CED-3 interface. Structural analysis together with published evidence strongly suggest a working model in which two molecules of CED-3 zymogen, through specific recognition, are forced into the hutch of the CED-4 apoptosome, consequently undergoing dimerization and autocatalytic maturation. The mechanism of CED-3 activation represents a major revision of the prevailing model for initiator caspase activation.

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Organizational Affiliation: 

Ministry of Education Protein Science Laboratory, Center for Structural Biology, School of Life Sciences.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell death protein 3	A, B	306	Caenorhabditis elegans	Mutation(s): 0  Gene Names: ced-3, C48D1.2 EC: 3.4.22 (PDB Primary Data), 3.4.22.60 (UniProt)
Find proteins for P42573 (Caenorhabditis elegans) Explore P42573  Go to UniProtKB:  P42573

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.260 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: I 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.07	α = 90
b = 121.07	β = 90
c = 58.47	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-08-15 
• Released Date: 2013-10-09 
Deposition Author(s): Xu, Y., Jeffrey, P.D., Shi, Y.G.

Revision History 

• Version 1.0: 2013-10-09
  Type: Initial release