5JUY

Active human apoptosome with procaspase-9


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 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
  • Primary Citation of Related Structures:  
    5JUY

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome cH, I, J, K, L, M, N104Bos taurusMutation(s): 0 
Gene Names: CYCSCYC
Find proteins for P62894 (Bos taurus)
Explore P62894 
Go to UniProtKB:  P62894
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Caspase-9O, P, Q, R95Homo sapiensMutation(s): 0 
Gene Names: CASP9MCH6
EC: 3.4.22.62
Find proteins for P55211 (Homo sapiens)
Explore P55211 
Go to UniProtKB:  P55211
NIH Common Fund Data Resources
PHAROS  P55211
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Apoptotic protease-activating factor 1A, B, C, D, E, F, G1248Homo sapiensMutation(s): 0 
Gene Names: APAF1KIAA0413
Find proteins for O14727 (Homo sapiens)
Explore O14727 
Go to UniProtKB:  O14727
NIH Common Fund Data Resources
PHAROS  O14727
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEC
Query on HEC

Download CCD File 
H, I, J, K, L, M, N
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
 Ligand Interaction
DTP
Query on DTP

Download CCD File 
A, B, C, D, E, F, G
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesRO1 GM63834

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-10-26
    Changes: Other
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2018-07-18
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-12-25
    Changes: Author supporting evidence