2A5Y

Structure of a CED-4/CED-9 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nature04002

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apoptosis regulator ced-9
A
204Caenorhabditis elegansMutation(s): 3 
Gene Names: ced-9
Find proteins for P41958 (Caenorhabditis elegans)
Go to UniProtKB:  P41958
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ced-4
B, C
549Caenorhabditis elegansMutation(s): 0 
Gene Names: ced-4
Find proteins for P30429 (Caenorhabditis elegans)
Go to UniProtKB:  P30429
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
B, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.249 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.898α = 90.00
b = 128.898β = 90.00
c = 209.928γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SOLVEphasing
HKL-2000data reduction
SCALEPACKdata scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance