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- PDB-1d2z: THREE-DIMENSIONAL STRUCTURE OF A COMPLEX BETWEEN THE DEATH DOMAIN... -

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Basic information

Entry
Database: PDB / ID: 1d2z
TitleTHREE-DIMENSIONAL STRUCTURE OF A COMPLEX BETWEEN THE DEATH DOMAINS OF PELLE AND TUBE
Components
  • DEATH DOMAIN OF PELLE
  • DEATH DOMAIN OF TUBE
KeywordsAPOPTOSIS / SIX-HELIX BUNDLE / LINEAR ARRAY OF DEATH DOMAINS / PLASTIC INTERFACES
Function / homology
Function and homology information


MyD88 dependent cascade initiated on endosome / determination of dorsal/ventral asymmetry / hemocyte proliferation / Formation of the trans-membrane 'signalling complex' / Adaptor protein complex binds to TL receptor at the plasma membrane / DL and DIF homodimers bind to TUB and phosphorylated PLL in the TL receptor 'signalling complex' / DL and DIF homodimers complexed with CACT are all phosphorylated in the TL receptor 'signalling complex' / Activated PLL kinase is autophosphorylated in the TL receptor 'signalling complex' / Phosphorylated CACT, DL and DIF homodimers dissociate from the TL receptor 'signalling complex' / PLL kinase binds to TUB in the TL receptor 'signalling complex' ...MyD88 dependent cascade initiated on endosome / determination of dorsal/ventral asymmetry / hemocyte proliferation / Formation of the trans-membrane 'signalling complex' / Adaptor protein complex binds to TL receptor at the plasma membrane / DL and DIF homodimers bind to TUB and phosphorylated PLL in the TL receptor 'signalling complex' / DL and DIF homodimers complexed with CACT are all phosphorylated in the TL receptor 'signalling complex' / Activated PLL kinase is autophosphorylated in the TL receptor 'signalling complex' / Phosphorylated CACT, DL and DIF homodimers dissociate from the TL receptor 'signalling complex' / PLL kinase binds to TUB in the TL receptor 'signalling complex' / positive regulation of antifungal peptide production / TAK1-dependent IKK and NF-kappa-B activation / activated TAK1 mediates p38 MAPK activation / IRAK1 recruits IKK complex / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / zygotic specification of dorsal/ventral axis / Interleukin-1 signaling / positive regulation of hippo signaling / larval somatic muscle development / histone H3T3 kinase activity / antifungal innate immune response / Toll signaling pathway / response to fungus / positive regulation of ubiquitin-dependent protein catabolic process / dorsal/ventral pattern formation / protein tyrosine kinase binding / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway / positive regulation of protein catabolic process / mitotic cell cycle / cellular response to lipopolysaccharide / protein autophosphorylation / non-specific serine/threonine protein kinase / intracellular signal transduction / protein domain specific binding / protein phosphorylation / protein serine kinase activity / innate immune response / protein serine/threonine kinase activity / apoptotic process / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tube, Death domain / Tube Death domain / Pelle, death domain / Death Domain, Fas / Death Domain, Fas / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily ...Tube, Death domain / Tube Death domain / Pelle, death domain / Death Domain, Fas / Death Domain, Fas / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein Tube / Serine/threonine-protein kinase pelle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsXiao, T. / Towb, P. / Wasserman, S.A. / Sprang, S.R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Three-dimensional structure of a complex between the death domains of Pelle and Tube.
Authors: Xiao, T. / Towb, P. / Wasserman, S.A. / Sprang, S.R.
History
DepositionSep 28, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEATH DOMAIN OF PELLE
B: DEATH DOMAIN OF TUBE
C: DEATH DOMAIN OF PELLE
D: DEATH DOMAIN OF TUBE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3005
Polymers59,0624
Non-polymers2381
Water4,792266
1
A: DEATH DOMAIN OF PELLE
B: DEATH DOMAIN OF TUBE


Theoretical massNumber of molelcules
Total (without water)29,5312
Polymers29,5312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-5 kcal/mol
Surface area12880 Å2
MethodPISA
2
C: DEATH DOMAIN OF PELLE
D: DEATH DOMAIN OF TUBE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7693
Polymers29,5312
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-3 kcal/mol
Surface area13610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.123, 87.495, 117.662
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DEATH DOMAIN OF PELLE


Mass: 12446.343 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli)
Keywords: THE FIRST FOUR RESIDUES OBSERVED IN THE STRUCTURE ORIGINATE FROM CLONING ARTEFACT.
References: UniProt: Q05652
#2: Protein DEATH DOMAIN OF TUBE


Mass: 17084.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: P22812
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 20-25% PEG 2000 monomethyl ether, 100 mM Hepes pH 7.2-8.4 0-200 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-25 %mPEG20001reservoir
2100 mMNa+-HEPES1reservoir
3200 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.981
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1999
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 41269 / Num. obs: 40020 / % possible obs: 95.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 35.92 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.7
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.499 / Num. unique all: 1998 / % possible all: 98.6
Reflection
*PLUS
% possible obs: 98.9 %
Reflection shell
*PLUS
% possible obs: 98.6 % / Mean I/σ(I) obs: 2.4

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Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→25 Å / Rfactor Rfree error: 0.004 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood target
RfactorNum. reflection% reflectionSelection details
Rfree0.244 3946 9.6 %RANDOM
Rwork0.211 ---
all0.22 41220 --
obs0.22 39471 95.6 %-
Solvent computationBsol: 32.426 Å2 / ksol: 0.33331 e/Å3
Displacement parametersBiso mean: 42.45 Å2
Baniso -1Baniso -2Baniso -3
1-7.61 Å20 Å20 Å2
2--3.02 Å20 Å2
3----10.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4105 0 15 266 4386
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.067
X-RAY DIFFRACTIONc_mcbond_it1.731.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it2.742
X-RAY DIFFRACTIONc_scangle_it3.612.5

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