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 1.3 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Death domain-containing protein CRADD ABCDEFG114Homo sapiensMutation(s): 0 
Gene Names: CRADDRAIDD
Find proteins for P78560 (Homo sapiens)
Explore P78560 
Go to UniProtKB:  P78560
NIH Common Fund Data Resources
PHAROS:  P78560
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Leucine-rich repeat and death domain-containing protein HIJKL118Homo sapiensMutation(s): 0 
Gene Names: LRDDPIDDPIDD1
EC: 3.4.21
Find proteins for Q9HB75 (Homo sapiens)
Explore Q9HB75 
Go to UniProtKB:  Q9HB75
NIH Common Fund Data Resources
PHAROS:  Q9HB75
Protein Feature View
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  • 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

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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