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- PDB-3u3s: The S-SAD phased crystal structure of the ecto-domain of Death Re... -

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Basic information

Entry
Database: PDB / ID: 3u3s
TitleThe S-SAD phased crystal structure of the ecto-domain of Death Receptor 6 (DR6)
ComponentsTumor necrosis factor receptor superfamily member 21
KeywordsAPOPTOSIS / trigger apoptosis
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
Tumor necrosis factor receptor superfamily member 21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsRu, H. / Zhao, L.X. / Ding, W. / Jiao, L.Y. / Shaw, N. / Zhang, L.G. / Hung, L.W. / Matsugaki, N. / Wakatsuki, S. / Liu, Z.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS.
Authors: Ru, H. / Zhao, L. / Ding, W. / Jiao, L. / Shaw, N. / Liang, W. / Zhang, L. / Hung, L.W. / Matsugaki, N. / Wakatsuki, S. / Liu, Z.J.
History
DepositionOct 6, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 21


Theoretical massNumber of molelcules
Total (without water)34,2121
Polymers34,2121
Non-polymers00
Water2,558142
1
A: Tumor necrosis factor receptor superfamily member 21

A: Tumor necrosis factor receptor superfamily member 21


Theoretical massNumber of molelcules
Total (without water)68,4232
Polymers68,4232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_585x,x-y+3,-z+1/61
Buried area1480 Å2
ΔGint-15 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.674, 77.674, 186.800
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-406-

HOH

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Components

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


Mass: 34211.570 Da / Num. of mol.: 1 / Fragment: cysteine rich domain
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) / References: UniProt: O75509
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.2M ammonium acetate, 0.1M sodium citrate tribasic dehydrate (pH5.0-6.0), 25-30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
PH range: 5.0-6.0

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 2 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 11, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 9308 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.892 / SU B: 8.357 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26006 469 4.8 %RANDOM
Rwork0.19652 ---
all0.2035 ---
obs0.19943 9308 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.033 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20.22 Å20 Å2
2--0.44 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 0 142 1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021269
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.9551733
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8035165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00523.8347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.71715209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.914158
X-RAY DIFFRACTIONr_chiral_restr0.120.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022943
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 27 -
Rwork0.284 555 -
obs--100 %

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