3LQR

Structure of CED-4:CED-3 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/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.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell death protein 4
A, B
549Caenorhabditis elegansMutation(s): 0 
Gene Names: ced-4
UniProt
Find proteins for P30429 (Caenorhabditis elegans)
Explore P30429 
Go to UniProtKB:  P30429
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30429
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.33α = 90
b = 181.33β = 90
c = 202.88γ = 90
Software Package:
Software NamePurpose
BSSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description