4RHW | pdb_00004rhw

Crystal structure of Apaf-1 CARD and caspase-9 CARD complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.226 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4RHW

This is version 1.2 of the entry. See complete history

Literature

Molecular determinants of caspase-9 activation by the Apaf-1 apoptosome.

Hu, Q.Wu, D.Chen, W.Yan, Z.Yan, C.He, T.Liang, Q.Shi, Y.

(2014) Proc Natl Acad Sci U S A 111: 16254-16261

  • DOI: https://doi.org/10.1073/pnas.1418000111
  • Primary Citation Related Structures: 
    4RHW

  • PubMed Abstract: 

    Autocatalytic activation of an initiator caspase triggers the onset of apoptosis. In dying cells, caspase-9 activation is mediated by a multimeric adaptor complex known as the Apaf-1 apoptosome. The molecular mechanism by which caspase-9 is activated by the Apaf-1 apoptosome remains largely unknown. Here we demonstrate that the previously reported 1:1 interaction between Apaf-1 caspase recruitment domain (CARD) and caspase-9 CARD is insufficient for the activation of caspase-9. Rather, formation of a multimeric CARD:CARD assembly between Apaf-1 and caspase-9, which requires three types of distinct interfaces, underlies caspase-9 activation. Importantly, an additional surface area on the multimeric CARD assembly is essential for caspase-9 activation. Together, these findings reveal mechanistic insights into the activation of caspase-9 by the Apaf-1 apoptosome and support the induced conformation model for initiator caspase activation by adaptor complexes.


  • Organizational Affiliation
    • Ministry of Education Protein Science Laboratory, Center for Structural Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China; and.

Macromolecule Content 

  • Total Structure Weight: 70.63 kDa 
  • Atom Count: 4,976 
  • Modeled Residue Count: 564 
  • Deposited Residue Count: 604 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Apoptotic protease-activating factor 1
A, B, C, D
97Homo 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:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Caspase-9
E, F
108Homo sapiensMutation(s): 0 
Gene Names: CASP9MCH6
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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth B]
J [auth B]
L [auth C]
G [auth A],
H [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C],
N [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
K [auth B],
O [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.226 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.531α = 90
b = 92.52β = 109.12
c = 68.031γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2018-10-17
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description