5JUY

Active human apoptosome with procaspase-9

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

A near atomic structure of the active human apoptosome.

Cheng, T.C., Hong, C., Akey, I.V., Yuan, S., Akey, C.W.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.17755

  • PubMed Abstract: 

    • In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo-electron microscopy. The resulting model gives insights ...

    In response to cell death signals, an active apoptosome is assembled from Apaf-1 and procaspase-9 (pc-9). Here we report a near atomic structure of the active human apoptosome determined by cryo-electron microscopy. The resulting model gives insights into cytochrome c binding, nucleotide exchange and conformational changes that drive assembly. During activation an acentric disk is formed on the central hub of the apoptosome. This disk contains four Apaf-1/pc-9 CARD pairs arranged in a shallow spiral with the fourth pc-9 CARD at lower occupancy. On average, Apaf-1 CARDs recruit 3 to 5 pc-9 molecules to the apoptosome and one catalytic domain may be parked on the hub, when an odd number of zymogens are bound. This suggests a stoichiometry of one or at most, two pc-9 dimers per active apoptosome. Thus, our structure provides a molecular framework to understand the role of the apoptosome in programmed cell death and disease.

    Organizational Affiliation: 

    Department of Physiology and Biophysics, Boston University School of Medicine, Boston, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apoptotic protease-activating factor 1
A, B, C, D, E, F, G
1248Homo 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
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Caspase-9
O, P, Q, R
95Homo sapiensMutation(s): 0 
Gene Names: CASP9 (MCH6)
EC: 3.4.22.62
Find proteins for P55211 (Homo sapiens)
Go to Gene View: CASP9
Go to UniProtKB:  P55211
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
HEC
Query on HEC
Download SDF File 
Download CCD File 
H, I, J, K, L, M, N
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 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 & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesRO1 GM63834

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-10-26
    Type: Other
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence
  • Version 1.3: 2018-07-18
    Type: Data collection, Experimental preparation