3SIP

Crystal structure of drICE and dIAP1-BIR1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural mechanisms of DIAP1 auto-inhibition and DIAP1-mediated inhibition of drICE.

Li, X.Wang, J.Shi, Y.

(2011) Nat Commun 2: 408-408

  • DOI: 10.1038/ncomms1418
  • Primary Citation of Related Structures:  
    3SIP, 3SIQ, 3SIR

  • PubMed Abstract: 
  • The Drosophila inhibitor of apoptosis protein DIAP1 exists in an auto-inhibited conformation, unable to suppress the effector caspase drICE. Auto-inhibition is disabled by caspase-mediated cleavage of DIAP1 after Asp20. The cleaved DIAP1 binds to mature drICE, inhibits its protease activity, and, presumably, also targets drICE for ubiquitylation ...

    The Drosophila inhibitor of apoptosis protein DIAP1 exists in an auto-inhibited conformation, unable to suppress the effector caspase drICE. Auto-inhibition is disabled by caspase-mediated cleavage of DIAP1 after Asp20. The cleaved DIAP1 binds to mature drICE, inhibits its protease activity, and, presumably, also targets drICE for ubiquitylation. DIAP1-mediated suppression of drICE is effectively antagonized by the pro-apoptotic proteins Reaper, Hid, and Grim (RHG). Despite rigorous effort, the molecular mechanisms behind these observations are enigmatic. Here we report a 2.4 Å crystal structure of uncleaved DIAP1-BIR1, which reveals how the amino-terminal sequences recognize a conserved surface groove in BIR1 to achieve auto-inhibition, and a 3.5 Å crystal structure of active drICE bound to cleaved DIAP1-BIR1, which provides a structural explanation to DIAP1-mediated inhibition of drICE. These structures and associated biochemical analyses, together with published reports, define the molecular determinants that govern the interplay among DIAP1, drICE and the RHG proteins.


    Organizational Affiliation

    Ministry of Education Protein Science Laboratory, Center for Structural Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CaspaseA, B [auth C]157Drosophila melanogasterMutation(s): 0 
Gene Names: DriceICECG7788
EC: 3.4.22
UniProt
Find proteins for O01382 (Drosophila melanogaster)
Explore O01382 
Go to UniProtKB:  O01382
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Apoptosis 1 inhibitorC [auth E], D [auth F]115Drosophila melanogasterMutation(s): 1 
Gene Names: Diap1Iap1thCG12284
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt
Find proteins for Q24306 (Drosophila melanogaster)
Explore Q24306 
Go to UniProtKB:  Q24306
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CaspaseE [auth B], F [auth D]109Drosophila melanogasterMutation(s): 0 
Gene Names: DriceICECG7788
EC: 3.4.22
UniProt
Find proteins for O01382 (Drosophila melanogaster)
Explore O01382 
Go to UniProtKB:  O01382
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth E], H [auth F]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.35α = 90
b = 148.115β = 90
c = 156.738γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2011-06-20 
  • Released Date: 2011-08-10 
  • Deposition Author(s): Li, X., Wang, J., Shi, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2013-07-10
    Changes: Database references
  • Version 1.2: 2014-05-21
    Changes: Other
  • Version 1.3: 2018-07-25
    Changes: Data collection, Source and taxonomy, Structure summary