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 2A5Y | pdb_00002a5y

Structure of a CED-4/CED-9 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.277 (Depositor) 
  • R-Value Work: 
    0.249 (Depositor) 
  • R-Value Observed: 
    0.249 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2A5Y

This is version 1.4 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1038/nature04002
  • Primary Citation Related Structures: 
    2A5Y

  • 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.


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

Macromolecule Content 

  • Total Structure Weight: 150.69 kDa 
  • Atom Count: 8,730 
  • Modeled Residue Count: 1,047 
  • Deposited Residue Count: 1,302 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Apoptosis regulator ced-9204Caenorhabditis elegansMutation(s): 3 
UniProt
Find proteins for P41958 (Caenorhabditis elegans)
Explore P41958 
Go to UniProtKB:  P41958
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41958
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ced-4
B, C
549Caenorhabditis elegansMutation(s): 0 
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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.277 (Depositor) 
  • R-Value Work:  0.249 (Depositor) 
  • R-Value Observed: 0.249 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.898α = 90
b = 128.898β = 90
c = 209.928γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-02-14
    Changes: Data collection