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- PDB-2of5: Oligomeric Death Domain complex -

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Basic information

Entry
Database: PDB / ID: 2of5
TitleOligomeric Death Domain complex
Components
  • Death domain-containing protein CRADD
  • Leucine-rich repeat and death domain-containing protein
KeywordsAPOPTOSIS / Death domain complex
Function / homology
Function and homology information


death domain binding / endopeptidase complex / death receptor binding / regulation of canonical NF-kappaB signal transduction / TP53 Regulates Transcription of Caspase Activators and Caspases / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extrinsic apoptotic signaling pathway via death domain receptors / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of apoptotic signaling pathway ...death domain binding / endopeptidase complex / death receptor binding / regulation of canonical NF-kappaB signal transduction / TP53 Regulates Transcription of Caspase Activators and Caspases / protein autoprocessing / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / extrinsic apoptotic signaling pathway via death domain receptors / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of apoptotic signaling pathway / apoptotic signaling pathway / cellular response to mechanical stimulus / activation of cysteine-type endopeptidase activity involved in apoptotic process / protein-macromolecule adaptor activity / positive regulation of NF-kappaB transcription factor activity / protease binding / regulation of apoptotic process / endopeptidase activity / positive regulation of apoptotic process / DNA damage response / apoptotic process / nucleolus / negative regulation of apoptotic process / Golgi apparatus / signal transduction / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Peptidase S68, pidd / Peptidase S68 / CRADD, Death domain / Death domain-containing protein CRADD / RAIDD, CARD domain / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death Domain, Fas / Death Domain, Fas ...Peptidase S68, pidd / Peptidase S68 / CRADD, Death domain / Death domain-containing protein CRADD / RAIDD, CARD domain / ZU5 domain / ZU5 domain / ZU5 domain profile. / Death Domain, Fas / Death Domain, Fas / Caspase recruitment domain / Death domain profile. / CARD domain / CARD caspase recruitment domain profile. / Caspase recruitment domain / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Death domain-containing protein CRADD / p53-induced death domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsPark, H.H. / Logette, E. / Raunser, S. / Cuenin, S. / Walz, T. / Tschopp, J. / Wu, H.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Death domain assembly mechanism revealed by crystal structure of the oligomeric PIDDosome core complex.
Authors: Park, H.H. / Logette, E. / Raunser, S. / Cuenin, S. / Walz, T. / Tschopp, J. / Wu, H.
History
DepositionJan 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Derived calculations
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Death domain-containing protein CRADD
B: Death domain-containing protein CRADD
C: Death domain-containing protein CRADD
D: Death domain-containing protein CRADD
E: Death domain-containing protein CRADD
F: Death domain-containing protein CRADD
G: Death domain-containing protein CRADD
H: Leucine-rich repeat and death domain-containing protein
I: Leucine-rich repeat and death domain-containing protein
J: Leucine-rich repeat and death domain-containing protein
K: Leucine-rich repeat and death domain-containing protein
L: Leucine-rich repeat and death domain-containing protein


Theoretical massNumber of molelcules
Total (without water)158,67512
Polymers158,67512
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.4, 138.4, 207.5
Angle α, β, γ (deg.)90, 90, 120
Int Tables number170
Space group name H-MP65
DetailsComplex are formed by 5 PIDD death domain and 7 RAIDD death domain without apparent symmetry

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Components

#1: Protein
Death domain-containing protein CRADD / Caspase and RIP adapter with death domain / RIP-associated protein with a death domain


Mass: 13095.815 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRADD, RAIDD / Plasmid: pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P78560
#2: Protein
Leucine-rich repeat and death domain-containing protein / p53-induced protein with a death domain


Mass: 13400.929 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRDD, PIDD / Plasmid: pET26b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9HB75
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.61 Å3/Da / Density % sol: 65.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5.5% PEG 3350, 200mM NaCl and 100mM Na/K phosphate buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C11.008
SYNCHROTRONNSLS X4A21.0079
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDAug 1, 2006mirrors
ADSC QUANTUM 42CCDMar 1, 2006mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0081
21.00791
ReflectionResolution: 3.2→30 Å / Num. all: 36257 / Num. obs: 28927 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.3 % / Biso Wilson estimate: 12 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.074 / Net I/σ(I): 15
Reflection shellResolution: 3.2→30 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.36 / % possible all: 95

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.2→30 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection
Rfree0.275 -
Rwork0.236 -
all-34580
obs-28345
Refinement stepCycle: LAST / Resolution: 3.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9096 0 0 21 9117
LS refinement shellResolution: 3.2→3.3 Å / Rfactor Rfree error: 0.012 /
Rfactor% reflection
Rfree0.275 -
Rwork0.236 -
obs-88 %

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