4M9S

crystal structure of CED-4 bound CED-3 fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.207 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.283 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Mechanistic insights into CED-4-mediated activation of CED-3.

Huang, W.Jiang, T.Choi, W.Qi, S.Pang, Y.Hu, Q.Xu, Y.Gong, X.Jeffrey, P.D.Wang, J.Shi, Y.

(2013) Genes Dev. 27: 2039-2048

  • DOI: 10.1101/gad.224428.113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Programmed cell death in Caenorhabditis elegans requires activation of the caspase CED-3, which strictly depends on CED-4. CED-4 forms an octameric apoptosome, which binds the CED-3 zymogen and facilitates its autocatalytic maturation. Despite recent ...

    Programmed cell death in Caenorhabditis elegans requires activation of the caspase CED-3, which strictly depends on CED-4. CED-4 forms an octameric apoptosome, which binds the CED-3 zymogen and facilitates its autocatalytic maturation. Despite recent advances, major questions remain unanswered. Importantly, how CED-4 recognizes CED-3 and how such binding facilitates CED-3 activation remain completely unknown. Here we demonstrate that the L2' loop of CED-3 directly binds CED-4 and plays a major role in the formation of an active CED-4-CED-3 holoenzyme. The crystal structure of the CED-4 apoptosome bound to the L2' loop fragment of CED-3, determined at 3.2 Å resolution, reveals specific interactions between a stretch of five hydrophobic amino acids from CED-3 and a shallow surface pocket within the hutch of the funnel-shaped CED-4 apoptosome. Structure-guided biochemical analysis confirms the functional importance of the observed CED-4-CED-3 interface. Structural analysis together with published evidence strongly suggest a working model in which two molecules of CED-3 zymogen, through specific recognition, are forced into the hutch of the CED-4 apoptosome, consequently undergoing dimerization and autocatalytic maturation. The mechanism of CED-3 activation represents a major revision of the prevailing model for initiator caspase activation.


    Organizational Affiliation

    Ministry of Education Protein Science Laboratory, Center for Structural Biology, School of Life Sciences.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell death protein 4
A, B, C, D
549Caenorhabditis elegansMutation(s): 0 
Gene Names: ced-4
Find proteins for P30429 (Caenorhabditis elegans)
Go to UniProtKB:  P30429
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CED-3 fragment
E, F, G, H
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

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

Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.207 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.283 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 178.814α = 90.00
b = 178.814β = 90.00
c = 201.125γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
ADSCdata collection
HKL-2000data reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-23
    Type: Initial release