5WVE

Apaf-1-Caspase-9 holoenzyme


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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

Mechanistic insights into caspase-9 activation by the structure of the apoptosome holoenzyme

Li, Y.Zhou, M.Hu, Q.Bai, X.-C.Huang, W.Scheres, S.H.W.Shi, Y.

(2017) Proc Natl Acad Sci U S A 114: 1542-1547

  • DOI: https://doi.org/10.1073/pnas.1620626114
  • Primary Citation of Related Structures:  
    5WVE

  • PubMed Abstract: 

    Mammalian intrinsic apoptosis requires activation of the initiator caspase-9, which then cleaves and activates the effector caspases to execute cell killing. The heptameric Apaf-1 apoptosome is indispensable for caspase-9 activation by together forming a holoenzyme. The molecular mechanism of caspase-9 activation remains largely enigmatic. Here, we report the cryoelectron microscopy (cryo-EM) structure of an apoptotic holoenzyme and structure-guided biochemical analyses. The caspase recruitment domains (CARDs) of Apaf-1 and caspase-9 assemble in two different ways: a 4:4 complex docks onto the central hub of the apoptosome, and a 2:1 complex binds the periphery of the central hub. The interface between the CARD complex and the central hub is required for caspase-9 activation within the holoenzyme. Unexpectedly, the CARD of free caspase-9 strongly inhibits its proteolytic activity. These structural and biochemical findings demonstrate that the apoptosome activates caspase-9 at least in part through sequestration of the inhibitory CARD domain.


  • Organizational Affiliation

    Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptotic protease-activating factor 1
A, C, E, G, I
A, C, E, G, I, K, M
1,248Homo sapiensMutation(s): 0 
Gene Names: APAF1KIAA0413
UniProt & NIH Common Fund Data Resources
Find proteins for O14727 (Homo sapiens)
Explore O14727 
Go to UniProtKB:  O14727
PHAROS:  O14727
GTEx:  ENSG00000120868 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14727
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c
B, D, F, H, J
B, D, F, H, J, L, N
105Equus caballusMutation(s): 0 
Gene Names: CYCSCYC
UniProt
Find proteins for P00004 (Equus caballus)
Explore P00004 
Go to UniProtKB:  P00004
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00004
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptotic protease-activating factor 1
O, P, Q, R, W
O, P, Q, R, W, X
102Homo sapiensMutation(s): 0 
Gene Names: APAF1KIAA0413
UniProt & NIH Common Fund Data Resources
Find proteins for O14727 (Homo sapiens)
Explore O14727 
Go to UniProtKB:  O14727
PHAROS:  O14727
GTEx:  ENSG00000120868 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14727
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase
S, T, U, V, Y
100Homo sapiensMutation(s): 0 
EC: 3.4.22.62
UniProt & NIH Common Fund Data Resources
Find proteins for P55211 (Homo sapiens)
Explore P55211 
Go to UniProtKB:  P55211
PHAROS:  P55211
GTEx:  ENSG00000132906 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55211
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
BA [auth B]
EA [auth D]
HA [auth F]
KA [auth H]
NA [auth J]
BA [auth B],
EA [auth D],
HA [auth F],
KA [auth H],
NA [auth J],
QA [auth L],
TA [auth N]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
DTP
Query on DTP

Download Ideal Coordinates CCD File 
CA [auth C]
FA [auth E]
IA [auth G]
LA [auth I]
OA [auth K]
CA [auth C],
FA [auth E],
IA [auth G],
LA [auth I],
OA [auth K],
RA [auth M],
Z [auth A]
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth A]
DA [auth C]
GA [auth E]
JA [auth G]
MA [auth I]
AA [auth A],
DA [auth C],
GA [auth E],
JA [auth G],
MA [auth I],
PA [auth K],
SA [auth M]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyChina2014ZX09507003006 to YS
National Natural Science Foundation of ChinaChina(projects 31430020, 31130002, and 31321062 to YS
UK Medical Research CouncilUnited Kingdom(MC_UP_A025_1013, to SHWS

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-03-01
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Derived calculations, Structure summary