4M9Z

Crystal structure of CED-4 bound CED-3 fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 

wwPDB Validation 3D Report Full Report



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
  • Structures With Same Primary Citation

  • 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: 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.

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-4C35D10.9
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 CCD File 
A, B, C, D
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

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: 3.40 Å
  • R-Value Free: 0.327 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.167α = 90
b = 178.167β = 90
c = 200.738γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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