4M9R

Crystal structure of CED-3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 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.G.

(2013) Genes Dev 27: 2039-2048

  • DOI: https://doi.org/10.1101/gad.224428.113
  • Primary Citation of Related Structures:  
    4M9R, 4M9S, 4M9X, 4M9Y, 4M9Z

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell death protein 3
A, B
306Caenorhabditis elegansMutation(s): 0 
Gene Names: ced-3
EC: 3.4.22 (PDB Primary Data), 3.4.22.60 (UniProt)
UniProt
Find proteins for P42573 (Caenorhabditis elegans)
Explore P42573 
Go to UniProtKB:  P42573
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42573
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.07α = 90
b = 121.07β = 90
c = 58.47γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description