2OF5

Oligomeric Death Domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Death domain assembly mechanism revealed by crystal structure of the oligomeric PIDDosome core complex.

Park, H.H.Logette, E.Raunser, S.Cuenin, S.Walz, T.Tschopp, J.Wu, H.

(2007) Cell 128: 533-546

  • DOI: https://doi.org/10.1016/j.cell.2007.01.019
  • Primary Citation of Related Structures:  
    2OF5

  • PubMed Abstract: 

    Proteins of the death domain (DD) superfamily mediate assembly of oligomeric signaling complexes for the activation of caspases and kinases via unknown mechanisms. Here we report the crystal structure of the PIDD DD and RAIDD DD complex, which forms the core of the caspase-2-activating complex PIDDosome. Although RAIDD DD and PIDD DD are monomers, they assemble into a complex that comprises seven RAIDD DDs and five PIDD DDs. Despite the use of an asymmetric assembly mechanism, all DDs in the complex are in quasi-equivalent environments. The structure provided eight unique asymmetric interfaces, which can be classified into three types. These three types of interactions together cover a majority of the DD surface. Mutagenesis on almost all interfaces leads to disruption of the assembly, resulting in defective caspase-2 activation. The three types of interactions may represent most, if not all, modes of interactions in the DD superfamily for assembling complexes of different stoichiometry.


  • Organizational Affiliation

    Weill Medical College, Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Death domain-containing protein CRADD
A, B, C, D, E
A, B, C, D, E, F, G
114Homo sapiensMutation(s): 0 
Gene Names: CRADDRAIDD
UniProt & NIH Common Fund Data Resources
Find proteins for P78560 (Homo sapiens)
Explore P78560 
Go to UniProtKB:  P78560
PHAROS:  P78560
GTEx:  ENSG00000169372 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78560
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat and death domain-containing protein
H, I, J, K, L
118Homo sapiensMutation(s): 0 
Gene Names: LRDDPIDD
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HB75 (Homo sapiens)
Explore Q9HB75 
Go to UniProtKB:  Q9HB75
PHAROS:  Q9HB75
GTEx:  ENSG00000177595 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HB75
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.236 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.4α = 90
b = 138.4β = 90
c = 207.5γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-09-18
    Changes: Derived calculations
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references