4M9S | pdb_00004m9s

crystal structure of CED-4 bound CED-3 fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 
    0.334 (Depositor), 0.364 (DCC) 
  • R-Value Work: 
    0.283 (Depositor), 0.314 (DCC) 
  • R-Value Observed: 
    0.285 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4M9S

Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1101/gad.224428.113
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 261.48 kDa 
  • Atom Count: 16,687 
  • Modeled Residue Count: 2,064 
  • Deposited Residue Count: 2,228 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cell death protein 4A,
C [auth B],
E [auth C],
G [auth D]
549Caenorhabditis elegansMutation(s): 0 
Gene Names: ced-4C35D10.9
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
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
CED-3 fragmentB [auth E],
D [auth F],
F [auth G],
H
8N/AMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP



Download:Ideal Coordinates CCD File
J [auth A],
L [auth B],
N [auth C],
P [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
I [auth A],
K [auth B],
M [auth C],
O [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
C [auth B],
E [auth C],
G [auth D]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free:  0.334 (Depositor), 0.364 (DCC) 
  • R-Value Work:  0.283 (Depositor), 0.314 (DCC) 
  • R-Value Observed: 0.285 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.814α = 90
b = 178.814β = 90
c = 201.125γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-23
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2023-12-06
    Changes: Data collection
  • Version 1.3: 2024-10-30
    Changes: Structure summary