Rapid Folding and Unfolding of Apaf-1 CARD

Experimental Data Snapshot

  • Resolution: 1.59 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.239 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Rapid Folding and Unfolding of Apaf-1 CARD.

Milam, S.L.Nicely, N.I.Feeney, B.Mattos, C.Clark, A.C.

(2007) J Mol Biol 369: 290-304

  • DOI: https://doi.org/10.1016/j.jmb.2007.02.105
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Caspase recruitment domains (CARDs) are members of the death domain superfamily and contain six antiparallel helices in an alpha-helical Greek key topology. We have examined the equilibrium and kinetic folding of the CARD of Apaf-1 (apoptotic protease activating factor 1), which consists of 97 amino acid residues, at pH 6 and pH 8. The results showed that an apparent two state equilibrium mechanism is not adequate to describe the folding of Apaf-1 CARD at either pH, suggesting the presence of intermediates in equilibrium unfolding. Interestingly, the results showed that the secondary structure is less stable than the tertiary structure, based on the transition mid-points for unfolding. Single mixing and sequential mixing stopped-flow studies showed that Apaf-1 CARD folds and unfolds rapidly and suggest a folding mechanism that contains parallel channels with two unfolded conformations folding to the native conformation. Kinetic simulations show that a slow folding phase is described by a third conformation in the unfolded ensemble that interconverts with one or both unfolded species. Overall, the native ensemble is formed rapidly upon refolding. This is in contrast to other CARDs in which folding appears to be dominated by formation of kinetic traps.

  • Organizational Affiliation

    Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptotic protease-activating factor 194Homo sapiensMutation(s): 0 
Gene Names: APAF1
UniProt & NIH Common Fund Data Resources
Find proteins for O14727 (Homo sapiens)
Explore O14727 
Go to UniProtKB:  O14727
GTEx:  ENSG00000120868 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14727
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.59 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.239 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.468α = 90
b = 47.515β = 90
c = 54.746γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description