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- PDB-3qo4: The Crystal Structure of Death Receptor 6 -

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Basic information

Entry
Database: PDB / ID: 3qo4
TitleThe Crystal Structure of Death Receptor 6
ComponentsTumor necrosis factor receptor superfamily member 21
KeywordsAPOPTOSIS / Tumor Necrosis Factor Receptor (TNFR) / Alzheimer s Disease / Ligand-Receptor-Recognition
Function / homology
Function and homology information


regulation of oligodendrocyte differentiation / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of myelination / B cell apoptotic process / axonal fasciculation / oligodendrocyte apoptotic process / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / humoral immune response ...regulation of oligodendrocyte differentiation / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of myelination / B cell apoptotic process / axonal fasciculation / oligodendrocyte apoptotic process / negative regulation of interleukin-10 production / negative regulation of B cell proliferation / humoral immune response / negative regulation of T cell proliferation / myelination / PPARA activates gene expression / cellular response to tumor necrosis factor / T cell receptor signaling pathway / neuron apoptotic process / adaptive immune response / axon / apoptotic process / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 21 / Tumor necrosis factor receptor 21, N-terminal / Tumor necrosis factor receptor 21, death domain / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region ...Tumour necrosis factor receptor 21 / Tumor necrosis factor receptor 21, N-terminal / Tumor necrosis factor receptor 21, death domain / Tumor Necrosis Factor Receptor, subunit A, domain 2 / Tumor Necrosis Factor Receptor, subunit A; domain 2 / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Putative ephrin-receptor like / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / Death-like domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Tumor necrosis factor receptor superfamily member 21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsKuester, M. / Kemmerzehl, S. / Dahms, S.O. / Roeser, D. / Than, M.E.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: The crystal structure of death receptor 6 (DR6): a potential receptor of the amyloid precursor protein (APP).
Authors: Kuester, M. / Kemmerzehl, S. / Dahms, S.O. / Roeser, D. / Than, M.E.
History
DepositionFeb 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 29, 2012Group: Database references
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED BY USING PYMOL'S DSS-FUNCTION
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED BY USING PYMOL'S DSS-FUNCTION

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8043
Polymers19,6481
Non-polymers1552
Water3,801211
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Tumor necrosis factor receptor superfamily member 21
hetero molecules

A: Tumor necrosis factor receptor superfamily member 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6076
Polymers39,2972
Non-polymers3104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area2120 Å2
ΔGint-46 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.910, 77.910, 187.844
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-293-

HOH

DetailsCONSIDERING A RATHER SMALL INTERFACE AREA OF 709 A2, ONLY TWO HYDROGEN BONDS AS ADDITIONAL STABILIZING CONTACTS AND MANY CONTACT MEDIATING WATER MOLECULES, WE CONCLUDE HOWEVER, THAT THE INTERACTION DETERMINED BY THE PISA SOFTWARE IS NOT OF PHYSIOLOGICAL RELEVANCE BUT RATHER IMPORTANT FOR STABILIZING THE DR6-CRD CRYSTALS

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Components

#1: Protein Tumor necrosis factor receptor superfamily member 21 / Death receptor 6


Mass: 19648.445 Da / Num. of mol.: 1 / Fragment: unp residues 42-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF21, DR6, UNQ437/PRO868 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2(DE3) / References: UniProt: O75509
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 4.19 Å3/Da / Density % sol: 70.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrate, 30% PEG4000, 0.5 M Ammoniumacetate , pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918, 1.03936, 1.04008, 1.04064
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 3, 2010
Details: double crystal monochromator with two sets of mirrors
RadiationMonochromator: Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9181
21.039361
31.040081
41.040641
ReflectionResolution: 2.1→29.982 Å / Num. obs: 20455 / % possible obs: 99.6 % / Redundancy: 3.2 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 11.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3 / % possible all: 98.2

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→29.7 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 917 -RANDOM
Rwork0.215 ---
all-17933 --
obs-17891 99.8 %-
Refinement stepCycle: LAST / Resolution: 2.2→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1222 0 9 211 1442
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0092
X-RAY DIFFRACTIONc_angle_deg1.61
LS refinement shellResolution: 2.2→2.24 Å / Rfactor Rfree: 0.361 / Rfactor Rwork: 0.314

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