3SFZ

Crystal structure of full-length murine Apaf-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of full-length Apaf-1: how the death signal is relayed in the mitochondrial pathway of apoptosis.

Reubold, T.F.Wohlgemuth, S.Eschenburg, S.

(2011) Structure 19: 1074-1083

  • DOI: 10.1016/j.str.2011.05.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The apoptotic protease-activating factor 1 (Apaf-1) relays the death signal in the mitochondrial pathway of apoptosis. Apaf-1 oligomerizes on binding of mitochondrially released cytochrome c into the heptameric apoptosome complex to ignite the downst ...

    The apoptotic protease-activating factor 1 (Apaf-1) relays the death signal in the mitochondrial pathway of apoptosis. Apaf-1 oligomerizes on binding of mitochondrially released cytochrome c into the heptameric apoptosome complex to ignite the downstream cascade of caspases. Here, we present the 3.0 Å crystal structure of full-length murine Apaf-1 in the absence of cytochrome c. The structure shows how the mammalian death switch is kept in its "off" position. By comparing the off state with a recent cryo-electron microscopy derived model of Apaf-1 in its apoptosomal conformation, we depict the molecular events that transform Apaf-1 from autoinhibited monomer to a building block of the caspase-activating apoptosome. Moreover, we have solved the crystal structure of the R265S mutant of full-length murine Apaf-1 in the absence of cytochrome c to 3.55 Å resolution and we show that proper function of Apaf-1 relies on R265 in the vicinity of the bound nucleotide.


    Organizational Affiliation

    Insitute for Biophysical Chemistry, Hannover Medical School, OE 4350, D-30625, Hannover, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apoptotic peptidase activating factor 1
A
1249Mus musculusMutation(s): 0 
Gene Names: Apaf1
Find proteins for O88879 (Mus musculus)
Go to UniProtKB:  O88879
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
GBL
Query on GBL

Download SDF File 
Download CCD File 
A
GAMMA-BUTYROLACTONE
DIHYDROFURAN-2(3H)-ONE
C4 H6 O2
YEJRWHAVMIAJKC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.650α = 90.00
b = 113.070β = 90.00
c = 243.560γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
CNSrefinement
PHASERphasing
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release