3D9T

CIAP1-BIR3 in complex with N-terminal peptide from Caspase-9 (ATPFQE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The structure of the BIR3 domain of cIAP1 in complex with the N-terminal peptides of SMAC and caspase-9.

Kulathila, R.Vash, B.Sage, D.Cornell-Kennon, S.Wright, K.Koehn, J.Stams, T.Clark, K.Price, A.

(2009) Acta Crystallogr D Biol Crystallogr 65: 58-66

  • DOI: https://doi.org/10.1107/S0907444908039243
  • Primary Citation of Related Structures:  
    3D9T, 3D9U

  • PubMed Abstract: 

    The inhibitor of apoptosis protein (IAP) family of molecules inhibit apoptosis through the suppression of caspase activity. It is known that the XIAP protein regulates both caspase-3 and caspase-9 through direct protein-protein interactions. Specifically, the BIR3 domain of XIAP binds to caspase-9 via a ;hotspot' interaction in which the N-terminal residues of caspase-9 bind in a shallow groove on the surface of XIAP. This interaction is regulated via SMAC, the N-terminus of which binds in the same groove, thus displacing caspase-9. The mechanism of suppression of apoptosis by cIAP1 is less clear. The structure of the BIR3 domain of cIAP1 (cIAP1-BIR3) in complex with N-terminal peptides from both SMAC and caspase-9 has been determined. The binding constants of these peptides to cIAP1-BIR3 have also been determined using the surface plasmon resonance technique. The structures show that the peptides interact with cIAP1 in the same way that they interact with XIAP: both peptides bind in a similar shallow groove in the BIR3 surface, anchored at the N-terminus by a charge-stabilized hydrogen bond. The binding data show that the SMAC and caspase-9 peptides bind with comparable affinities (85 and 48 nM, respectively).


  • Organizational Affiliation

    Novartis Institutes for Biomedical Research Inc., USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing protein 2
A, B
97Homo sapiensMutation(s): 0 
Gene Names: BIRC2API1IAP2MIHBRNF48
UniProt & NIH Common Fund Data Resources
Find proteins for Q13490 (Homo sapiens)
Explore Q13490 
Go to UniProtKB:  Q13490
GTEx:  ENSG00000110330 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13490
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Caspase-9
C, D
6N/AMutation(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
GTEx:  ENSG00000132906 
Entity Groups  
UniProt GroupP55211
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.268α = 90
b = 68.427β = 90
c = 122.358γ = 90
Software Package:
Software NamePurpose
CNXrefinement
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description