3LQQ

Structure of the CED-4 Apoptosome


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell death protein 4A, B549Caenorhabditis elegansMutation(s): 0 
Gene Names: ced-4C35D10.9
UniProt
Find proteins for P30429 (Caenorhabditis elegans)
Explore P30429 
Go to UniProtKB:  P30429
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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 = 181.64α = 90
b = 181.64β = 90
c = 203.19γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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