2P1H

Rapid Folding and Unfolding of Apaf-1 CARD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1016/j.jmb.2007.02.105

  • 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 proteas ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apoptotic protease-activating factor 1
A
94Homo sapiensGene Names: APAF1 (KIAA0413)
Find proteins for O14727 (Homo sapiens)
Go to Gene View: APAF1
Go to UniProtKB:  O14727
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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 = 90.00
b = 47.515β = 90.00
c = 54.746γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CNSphasing
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description