3SIP | pdb_00003sip

Crystal structure of drICE and dIAP1-BIR1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.256 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1038/ncomms1418
  • Primary Citation 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. 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.

Macromolecule Content 

  • Total Structure Weight: 87.4 kDa 
  • Atom Count: 5,714 
  • Modeled Residue Count: 712 
  • Deposited Residue Count: 762 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CaspaseA,
B [auth C]
157Drosophila melanogasterMutation(s): 0 
EC: 3.4.22
UniProt
Find proteins for O01382 (Drosophila melanogaster)
Explore O01382 
Go to UniProtKB:  O01382
Entity Groups
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UniProt GroupO01382
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Apoptosis 1 inhibitorC [auth E],
D [auth F]
115Drosophila melanogasterMutation(s): 1 
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
Entity Groups
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UniProt GroupQ24306
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
CaspaseE [auth B],
F [auth D]
109Drosophila melanogasterMutation(s): 0 
EC: 3.4.22
UniProt
Find proteins for O01382 (Drosophila melanogaster)
Explore O01382 
Go to UniProtKB:  O01382
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO01382
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.256 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
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

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
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description