Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.66 kDa 
• Atom Count: 3120 
• Modelled Residue Count: 340 
• Deposited Residue Count: 384 
• Unique protein chains: 1

4TX5

Crystal structure of Smac-DIABLO (in space group P65)

• PDB DOI: 10.2210/pdb4TX5/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-02 Released: 2015-07-15 
• Deposition Author(s): Milani, M., Mastangelo, E., Cossu, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.202 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

The activator of apoptosis Smac-DIABLO acts as a tetramer in solution.

Mastrangelo, E., Vachette, P., Cossu, F., Malvezzi, F., Bolognesi, M., Milani, M.

(2015) Biophys J 108: 714-723

• PubMed: 25650938 
• DOI: 10.1016/j.bpj.2014.11.3471
• Primary Citation of Related Structures:  
  4TX5


• PubMed Abstract: 
  

Smac-DIABLO in its mature form (20.8 kDa) binds to baculoviral IAP repeat (BIR) domains of inhibitor of apoptosis proteins (IAPs) releasing their inhibitory effects on caspases, thus promoting cell death. Despite its apparent molecular mass (∼100 kDa), Smac-DIABLO was held to be a dimer in solution, simultaneously targeting two distinct BIR domains. We report an extensive biophysical characterization of the protein alone and in complex with the X-linked IAP (XIAP)-BIR2-BIR3 domains. Our data show that Smac-DIABLO adopts a tetrameric assembly in solution and that the tetramer is able to bind two BIR2-BIR3 pairs of domains. Our small-angle x-ray scattering-based tetrameric model of Smac-DIABLO/BIR2-BIR3 highlights some conformational freedom of the complex that may be related to optimization of IAPs binding.

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Organizational Affiliation: 

Dipartimento di Bioscienze, Università di Milano, Milano, Italy; CNR-IBF, Istituto di Biofisica, Milano, Italy. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diablo homolog, mitochondrial	A, B	192	Homo sapiens	Mutation(s): 0  Gene Names: DIABLO, SMAC
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR28 (Homo sapiens) Explore Q9NR28  Go to UniProtKB:  Q9NR28
PHAROS:  Q9NR28

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	G [auth A], H [auth A], I [auth A], L [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.202 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.999	α = 90
b = 90.999	β = 90
c = 113.802	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-07-02 
• Released Date: 2015-07-15 
Deposition Author(s): Milani, M., Mastangelo, E., Cossu, F.

Revision History  

• Version 1.0: 2015-07-15
  Type: Initial release