Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 8-mer - A8 

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

Macromolecule Content

• Total Structure Weight: 126.97 kDa 
• Atom Count: 8124 
• Modelled Residue Count: 1004 
• Deposited Residue Count: 1098 
• Unique protein chains: 1

3LQQ

Structure of the CED-4 Apoptosome

• DOI: 10.2210/pdb3LQQ/pdb

• Classification: APOPTOSIS
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-09 Released: 2010-04-28 
• Deposition Author(s): Qi, S., Pang, Y., Shi, Y., Yan, N., Liu, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.53 Å
• R-Value Free: 0.311 
• R-Value Work: 0.275 
• R-Value Observed: 0.277 

Literature

Crystal structure of the Caenorhabditis elegans apoptosome reveals an octameric assembly of CED-4.

Qi, S., Pang, Y., Hu, Q., Liu, Q., Li, H., Zhou, Y., He, T., Liang, Q., Liu, Y., Yuan, X., Luo, G., Li, H., Wang, J., Yan, N., Shi, Y.

(2010) Cell 141: 446-457

• PubMed: 20434985 
• DOI: 10.1016/j.cell.2010.03.017
• Primary Citation of Related Structures:  
  3LQQ, 3LQR


• PubMed Abstract: 
  

The CED-4 homo-oligomer or apoptosome is required for initiation of programmed cell death in Caenorhabditis elegans by facilitating autocatalytic activation of the CED-3 caspase zymogen. How the CED-4 apoptosome assembles and activates CED-3 remains enigmatic. Here we report the crystal structure of the complete CED-4 apoptosome and show that it consists of eight CED-4 molecules, organized as a tetramer of an asymmetric dimer via a previously unreported interface among AAA(+) ATPases. These eight CED-4 molecules form a funnel-shaped structure. The mature CED-3 protease is monomeric in solution and forms an active holoenzyme with the CED-4 apoptosome, within which the protease activity of CED-3 is markedly stimulated. Unexpectedly, the octameric CED-4 apoptosome appears to bind only two, not eight, molecules of mature CED-3. The structure of the CED-4 apoptosome reveals shared principles for the NB-ARC family of AAA(+) ATPases and suggests a mechanism for the activation of CED-3.

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Organizational Affiliation: 

Ministry of Education Protein Science Laboratory, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell death protein 4	A, B	549	Caenorhabditis elegans	Mutation(s): 0  Gene Names: ced-4, C35D10.9
Find proteins for P30429 (Caenorhabditis elegans) Explore P30429  Go to UniProtKB:  P30429

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.53 Å
• R-Value Free: 0.311 
• R-Value Work: 0.275 
• R-Value Observed: 0.277 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.64	α = 90
b = 181.64	β = 90
c = 203.19	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-02-09 
• Released Date: 2010-04-28 
Deposition Author(s): Qi, S., Pang, Y., Shi, Y., Yan, N., Liu, Q.

Revision History  

• Version 1.0: 2010-04-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance