4EB9

cIAP1-BIR3 in complex with a divalent Smac mimetic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural insight into inhibitor of apoptosis proteins recognition by a potent divalent smac-mimetic.

Cossu, F.Milani, M.Vachette, P.Malvezzi, F.Grassi, S.Lecis, D.Delia, D.Drago, C.Seneci, P.Bolognesi, M.Mastrangelo, E.

(2012) Plos One 7: e49527-e49527

  • DOI: 10.1371/journal.pone.0049527
  • Primary Citation of Related Structures:  4EC4

  • PubMed Abstract: 
  • Genetic alterations enhancing cell survival and suppressing apoptosis are hallmarks of cancer that significantly reduce the efficacy of chemotherapy or radiotherapy. The Inhibitor of Apoptosis Protein (IAP) family hosts conserved proteins in the apop ...

    Genetic alterations enhancing cell survival and suppressing apoptosis are hallmarks of cancer that significantly reduce the efficacy of chemotherapy or radiotherapy. The Inhibitor of Apoptosis Protein (IAP) family hosts conserved proteins in the apoptotic pathway whose over-expression, frequently found in tumours, potentiates survival and resistance to anticancer agents. In humans, IAPs comprise eight members hosting one or more structural Baculoviral IAP Repeat (BIR) domains. Cellular IAPs (cIAP1 and 2) indirectly inhibit caspase-8 activation, and regulate both the canonical and the non-canonical NF-κB signaling pathways. In contrast to cIAPs, XIAP (X chromosome-linked Inhibitor of Apoptosis Protein) inhibits directly the effector caspases-3 and -7 through its BIR2 domain, and initiator caspase-9 through its BIR3 domain; molecular docking studies suggested that Smac/DIABLO antagonizes XIAP by simultaneously targeting both BIR2 and BIR3 domains. Here we report analytical gel filtration, crystallographic and SAXS experiments on cIAP1-BIR3, XIAP-BIR3 and XIAP-BIR2BIR3 domains, alone and in the presence of compound 9a, a divalent homodimeric Smac mimetic. 9a is shown to bind two BIR domains inter- (in the case of two BIR3) and intra-molecularly (in the case of XIAP-BIR2BIR3), with higher affinity for cIAP1-BIR3, relative to XIAP-BIR3. Despite the different crystal lattice packing, 9a maintains a right handed helical conformation in both cIAP1-BIR3 and XIAP-BIR3 crystals, that is likely conserved in solution as shown by SAXS data. Our structural results demonstrate that the 9a linker length, its conformational degrees of freedom and its hydrophobicity, warrant an overall compact structure with optimal solvent exposure of its two active moieties for IAPs binding. Our results show that 9a is a good candidate for pre-clinical and clinical studies, worth of further investigations in the field of cancer therapy.


    Organizational Affiliation

    Department of Biosciences, University of Milano, Milano, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Baculoviral IAP repeat-containing protein 2
A, B, C, D
122Homo sapiensGene Names: BIRC2 (API1, IAP2, MIHB, RNF48)
EC: 6.3.2.-
Find proteins for Q13490 (Homo sapiens)
Go to Gene View: BIRC2
Go to UniProtKB:  Q13490
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
0O6
Query on 0O6

Download SDF File 
Download CCD File 
C, D
(3S,6S,7S,9aS,3'S,6'S,7'S,9a'S)-N,N'-(benzene-1,4-diylbis{butane-4,1-diyl-1H-1,2,3-triazole-1,4-diyl[(S)-phenylmethanediyl]})bis[7-(hydroxymethyl)-6-{[(2S)-2-(methylamino)butanoyl]amino}-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide]
C64 H88 N14 O8
XKEIDWZKJDOBEL-OKDMWEIPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0O6IC50: 5.4 nM (99) BINDINGDB
0O6IC50: 5.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.322 
  • R-Value Work: 0.257 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.110α = 90.00
b = 81.310β = 95.67
c = 96.880γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
DNAdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release