2OF5 Apoptosis date Jan 02, 2007
title Oligomeric Death Domain Complex
authors H.H.Park, E.Logette, S.Raunser, S.Cuenin, T.Walz, J.Tschopp, H.Wu
compound source
Molecule: Death Domain-Containing Protein Cradd
Chain: A, B, C, D, E, F, G
Synonym: Caspase And Rip Adapter With Death Domain, Rip-Ass Protein With A Death Domain;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cradd, Raidd
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b

Molecule: Leucine-Rich Repeat And Death Domain-Containing P
Chain: H, I, J, K, L
Synonym: P53-Induced Protein With A Death Domain
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lrdd, Pidd
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet26b
symmetry Space Group: P 65
R_factor 0.236 R_Free 0.275
crystal
cell
length a length b length c angle alpha angle beta angle gamma
138.400 138.400 207.500 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.20 Å
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B, C, D, G


J, K, H, I, L


Primary referenceDeath domain assembly mechanism revealed by crystal structure of the oligomeric PIDDosome core complex., Park HH, Logette E, Raunser S, Cuenin S, Walz T, Tschopp J, Wu H, Cell. 2007 Feb 9;128(3):533-46. PMID:17289572
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (190 Kb) [Save to disk]
  • Biological Unit Coordinates (2of5.pdb1.gz) 183 Kb
  • CSU: Contacts of Structural Units for 2OF5
  • Likely Quarternary Molecular Structure file(s) for 2OF5
  • Structure Factors (482 Kb)
  • Retrieve 2OF5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OF5 from S2C, [Save to disk]
  • Re-refined 2of5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2OF5 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2OF5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2OF5, from MSDmotif at EBI
  • Fold representative 2of5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2of5_J] [2of5_A] [2of5_H] [2of5_K] [2of5_G] [2of5_F] [2of5_D] [2of5_B] [2of5_C] [2of5] [2of5_I] [2of5_E] [2of5_L]
  • SWISS-PROT database: [P78560] [Q9HB75]
  • Domain organization of [CRADD_HUMAN] [PIDD_HUMAN] by SWISSPFAM
  • Domain found in 2OF5: [DEATH ] by SMART
  • Other resources with information on 2OF5
  • Community annotation for 2OF5 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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