5WVC

Structure of the CARD-CARD disk


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural Insights into DD-Fold Assembly and Caspase-9 Activation by the Apaf-1 Apoptosome.

Su, T.W.Yang, C.Y.Kao, W.P.Kuo, B.J.Lin, S.M.Lin, J.Y.Lo, Y.C.Lin, S.C.

(2017) Structure 25: 407-420

  • DOI: https://doi.org/10.1016/j.str.2016.12.019
  • Primary Citation of Related Structures:  
    5WVC

  • PubMed Abstract: 

    Death domain (DD)-fold assemblies play a crucial role in regulating the signaling to cell survival or death. Here we report the crystal structure of the caspase recruitment domain (CARD)-CARD disk of the human apoptosome. The structure surprisingly reveals that three 1:1 Apaf-1:procaspase-9 CARD protomers form a novel helical DD-fold assembly on the heptameric wheel-like platform of the apoptosome. The small-angle X-ray scattering and multi-angle light scattering data also support that three protomers could form an oligomeric complex similar to the crystal structure. Interestingly, the quasi-equivalent environment of CARDs could generate different quaternary CARD assemblies. We also found that the type II interaction is conserved in all DD-fold complexes, whereas the type I interaction is found only in the helical DD-fold assemblies. This study provides crucial insights into the caspase activation mechanism, which is tightly controlled by a sophisticated and highly evolved CARD assembly on the apoptosome, and also enables better understanding of the intricate DD-fold assembly.


  • Organizational Affiliation

    Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics Program, Taiwan International Graduate Program, Academia, Sinica, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptotic protease-activating factor 1A [auth C],
C [auth A],
E
95Homo 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CaspaseB [auth D],
D [auth B],
F
151Homo 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download Ideal Coordinates CCD File 
G [auth C]
H [auth C]
I [auth D]
J [auth D]
K [auth D]
G [auth C],
H [auth C],
I [auth D],
J [auth D],
K [auth D],
L [auth D],
M [auth B],
N [auth B],
O [auth E],
P [auth F],
Q [auth F]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSO
Query on CSO
B [auth D],
D [auth B],
F
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.11α = 90
b = 190.11β = 90
c = 68.828γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academia SinciaTaiwanAS-102-TP-B14-1
Academia SinicaTaiwanAS-102-TP-B14-2
Academia SinicaTaiwanAS-102-TP-B14
MoSTTaiwan101-2320-B-001-034-MY3
MoSTTaiwan104-2320-B-001-020-MY3
MoSTTaiwan101-2311-B-006-008-MY3
MoSTTaiwan104-2320-B-006-033-MY3

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Database references, Structure summary