3J2T

An improved model of the human apoptosome

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Changes in apaf-1 conformation that drive apoptosome assembly.

Yuan, S., Topf, M., Reubold, T.F., Eschenburg, S., Akey, C.W.

(2013) Biochemistry 52: 2319-2327

  • DOI: 10.1021/bi301721g

  • PubMed Abstract: 

    • Apoptosome assembly is highly regulated in the intrinsic cell death pathway. To better understand this step, we created an improved model of the human apoptosome using a crystal structure of full length Apaf-1 and a single particle, electron density ...

    Apoptosome assembly is highly regulated in the intrinsic cell death pathway. To better understand this step, we created an improved model of the human apoptosome using a crystal structure of full length Apaf-1 and a single particle, electron density map at ~9.5 Å resolution. The apoptosome model includes N-terminal domains of Apaf-1, cognate β-propellers, and cytochrome c. A direct comparison of Apaf-1 in the apoptosome and as a monomer reveals conformational changes that occur during the first two steps of assembly. This includes an induced-fit mechanism for cytochrome c binding to regulatory β-propellers, which is dependent on shape and charge complementarity, and a large rotation of the nucleotide binding module during nucleotide exchange. These linked conformational changes create an extended Apaf-1 monomer and drive apoptosome assembly. Moreover, the N-terminal CARD in the inactive Apaf-1 monomer is not shielded from other proteins by β-propellers. Hence, the Apaf-1 CARD may be free to interact with a procaspase-9 CARD either before or during apoptosome assembly. Irrespective of the timing, the end product of assembly is a holo-apoptosome with an acentric CARD-CARD disk and tethered pc-9 catalytic domains. Subsequent activation of pc-9 leads to a proteolytic cascade and cell death.

    Related Citations: 
    • Structure of an apoptosome-procaspase-9 CARD complex.
      Yuan, S.,Yu, X.,Topf, M.,Ludtke, S.J.,Wang, X.,Akey, C.W.
      (2010) Structure 18: 571

    Organizational Affiliation: 

    Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apoptotic protease-activating factor 1
A, B, C, D, E, F, G
1263Homo sapiensMutation(s): 0 
Gene Names: APAF1 (KIAA0413)
Find proteins for O14727 (Homo sapiens)
Go to Gene View: APAF1
Go to UniProtKB:  O14727
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c
H, I, J, K, L, M, N
104Bos taurusMutation(s): 0 
Gene Names: CYCS (CYC)
Find proteins for P62894 (Bos taurus)
Go to Gene View: CYCS
Go to UniProtKB:  P62894
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
HEM
Query on HEM
Download SDF File 
Download CCD File 
H, I, J, K, L, M, N
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-04-17
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Data collection