3SHF

Crystal structure of the R265S mutant of full-length murine Apaf-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 
    0.305 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.230 (DCC) 

Starting Model: experimental
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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: https://doi.org/10.1016/j.str.2011.05.013
  • Primary Citation of Related Structures:  
    3SFZ, 3SHF

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptotic peptidase activating factor 11,256Mus musculusMutation(s): 1 
Gene Names: Apaf1
UniProt
Find proteins for O88879 (Mus musculus)
Explore O88879 
Go to UniProtKB:  O88879
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO88879
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free:  0.305 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.230 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.88α = 90
b = 111.82β = 90
c = 244.27γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted ADPClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-06
    Changes: Structure summary