Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 18-mer - A7B7C4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1127.66 kDa 
• Atom Count: 76058 
• Residue Count: 9461 
• Unique protein chains: 3

5JUY

Active human apoptosome with procaspase-9

• DOI: 10.2210/pdb5JUY/pdb
• EMDataResource: EMD-8178

• Classification: APOPTOSIS
• Organism(s): Homo sapiens, Bos taurus
• Expression System: Spodoptera frugiperda, Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-05-10 Released: 2016-10-19 
• Deposition Author(s): Cheng, T.C., Hong, C., Akey, I.V., Yuan, S., Akey, C.W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

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

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

• PubMed: 27697150 
• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apoptotic protease-activating factor 1	A, B, C, D, E, F, G	1248	Homo sapiens	Mutation(s): 0  Gene Names: APAF1, KIAA0413
Find proteins for O14727 (Homo sapiens) Explore O14727  Go to UniProtKB:  O14727
NIH Common Fund Data Resources
PHAROS:  O14727 GTEx:  ENSG00000120868

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c	H, I, J, K, L, M, N	104	Bos taurus	Mutation(s): 0  Gene Names: CYCS, CYC
Find proteins for P62894 (Bos taurus) Explore P62894  Go to UniProtKB:  P62894

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-9	O, P, Q, R	95	Homo sapiens	Mutation(s): 0  Gene Names: CASP9, MCH6 EC: 3.4.22.62
Find proteins for P55211 (Homo sapiens) Explore P55211  Go to UniProtKB:  P55211
NIH Common Fund Data Resources
PHAROS:  P55211 GTEx:  ENSG00000132906

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEC	H, I, J, K, L, M, N	HEME C C34 H34 Fe N4 O4 HXQIYSLZKNYNMH-LJNAALQVSA-N
DTP	A, B, C, D, E, F, G	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H16 N5 O12 P3 SUYVUBYJARFZHO-RRKCRQDMSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-05-10 
• Released Date: 2016-10-19 
Deposition Author(s): Cheng, T.C., Hong, C., Akey, I.V., Yuan, S., Akey, C.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	RO1 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