3EB5 | pdb_00003eb5

Structure of the cIAP2 RING domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.275 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.213 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3EB5

This is version 1.2 of the entry. See complete history

Literature

Structures of the cIAP2 RING domain reveal conformational changes associated with ubiquitin-conjugating enzyme (E2) recruitment.

Mace, P.D.Linke, K.Feltham, R.Schumacher, F.R.Smith, C.A.Vaux, D.L.Silke, J.Day, C.L.

(2008) J Biological Chem 283: 31633-31640

  • DOI: https://doi.org/10.1074/jbc.M804753200
  • Primary Citation Related Structures: 
    3EB5, 3EB6

  • PubMed Abstract: 

    Inhibitor of apoptosis (IAP) proteins are key negative regulators of cell death that are highly expressed in many cancers. Cell death caused by antagonists that bind to IAP proteins is associated with their ubiquitylation and degradation. The RING domain at the C terminus of IAP proteins is pivotal. Here we report the crystal structures of the cIAP2 RING domain homodimer alone, and bound to the ubiquitin-conjugating (E2) enzyme UbcH5b. These structures show that small changes in the RING domain accompany E2 binding. By mutating residues at the E2-binding surface, we show that autoubiquitylation is required for regulation of IAP abundance. Dimer formation is also critical, and mutation of a single C-terminal residue abrogated dimer formation and E3 ligase activity was diminished. We further demonstrate that disruption of E2 binding, or dimerization, stabilizes IAP proteins against IAP antagonists in vivo.


  • Organizational Affiliation
    • Biochemistry Department, University of Otago, Dunedin 9054, New Zealand.

Macromolecule Content 

  • Total Structure Weight: 8.39 kDa 
  • Atom Count: 551 
  • Modeled Residue Count: 65 
  • Deposited Residue Count: 74 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing protein 374Homo sapiensMutation(s): 0 
Gene Names: BIRC3API2IAP1MIHCRNF49
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q13489 (Homo sapiens)
Explore Q13489 
Go to UniProtKB:  Q13489
PHAROS:  Q13489
GTEx:  ENSG00000023445 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13489
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.275 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.213 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.869α = 90
b = 66.474β = 90
c = 77.465γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations