Biological Assembly 1  

 3D View: Structure | Electron Density

Pseudo Symmetry: Helical - H  (3D View)
Pseudo Stoichiometry: Homo 12-mer - A12 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A7B5 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 158.68 kDa 
• Atom Count: 9117 
• Modelled Residue Count: 1137 
• Deposited Residue Count: 1388 
• Unique protein chains: 2

2OF5

Oligomeric Death Domain complex

• DOI: 10.2210/pdb2OF5/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-01-02 Released: 2007-04-17 
• Deposition Author(s): Park, H.H., Logette, E., Raunser, S., Cuenin, S., Walz, T., Tschopp, J., Wu, H.

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Experimental Data Snapshot

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

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

• PubMed: 17289572 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Death domain-containing protein CRADD	A, B, C, D, E, F, G	114	Homo sapiens	Mutation(s): 0  Gene Names: CRADD, RAIDD
Find proteins for P78560 (Homo sapiens) Explore P78560  Go to UniProtKB:  P78560
NIH Common Fund Data Resources
PHAROS:  P78560 GTEx:  ENSG00000169372

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat and death domain-containing protein	H, I, J, K, L	118	Homo sapiens	Mutation(s): 0  Gene Names: LRDD, PIDD, PIDD1 EC: 3.4.21
Find proteins for Q9HB75 (Homo sapiens) Explore Q9HB75  Go to UniProtKB:  Q9HB75
NIH Common Fund Data Resources
PHAROS:  Q9HB75 GTEx:  ENSG00000177595

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 = 138.4	α = 90
b = 138.4	β = 90
c = 207.5	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-02 
• Released Date: 2007-04-17 
Deposition Author(s): Park, H.H., Logette, E., Raunser, S., Cuenin, S., Walz, T., Tschopp, J., Wu, H.

Revision History  

• 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