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- PDB-5ju5: Crystal structure of the human Tankyrase 1 (TNKS) SAM domain (D10... -

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Basic information

Entry
Database: PDB / ID: 5ju5
TitleCrystal structure of the human Tankyrase 1 (TNKS) SAM domain (D1055R), crystal form 1
ComponentsTankyrase-1
KeywordsSIGNALING PROTEIN / Tankyrase polymerisation / Wnt signalling / Poly(ADP-ribose)polymerase (PARP) / transferase
Function / homology
Function and homology information


negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material ...negative regulation of telomeric DNA binding / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / regulation of telomere maintenance via telomerase / XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / protein poly-ADP-ribosylation / pericentriolar material / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+-protein poly-ADP-ribosyltransferase activity / mRNA transport / spindle assembly / nuclear pore / : / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / mitotic spindle organization / TCF dependent signaling in response to WNT / Degradation of AXIN / peptidyl-threonine phosphorylation / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / protein transport / positive regulation of canonical Wnt signaling pathway / histone binding / peptidyl-serine phosphorylation / nuclear membrane / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / cell division / Golgi membrane / Golgi apparatus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Transcription Factor, Ets-1 / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily ...Transcription Factor, Ets-1 / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGuetter, S. / Mariotti, L. / Cronin, N.
CitationJournal: Mol.Cell / Year: 2016
Title: Tankyrase Requires SAM Domain-Dependent Polymerization to Support Wnt-beta-Catenin Signaling.
Authors: Mariotti, L. / Templeton, C.M. / Ranes, M. / Paracuellos, P. / Cronin, N. / Beuron, F. / Morris, E. / Guettler, S.
History
DepositionMay 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Source and taxonomy / Structure summary
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tankyrase-1
B: Tankyrase-1
C: Tankyrase-1
D: Tankyrase-1
E: Tankyrase-1
F: Tankyrase-1


Theoretical massNumber of molelcules
Total (without water)53,1246
Polymers53,1246
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-8 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.237, 55.222, 83.046
Angle α, β, γ (deg.)90.00, 96.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tankyrase-1 / TANK1 / ADP-ribosyltransferase diphtheria toxin-like 5 / ARTD5 / Poly [ADP-ribose] polymerase 5A / ...TANK1 / ADP-ribosyltransferase diphtheria toxin-like 5 / ARTD5 / Poly [ADP-ribose] polymerase 5A / TNKS-1 / TRF1-interacting ankyrin-related ADP-ribose polymerase / Tankyrase I


Mass: 8854.058 Da / Num. of mol.: 6 / Fragment: UNP residues 1018-1093
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS, PARP5A, PARPL, TIN1, TINF1, TNKS1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95271, NAD+ ADP-ribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Bis-Tris pH 5.5 0.2 M Magnesium chloride PEG 3350 25%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.5→82.57 Å / Num. obs: 16507 / % possible obs: 100 % / Redundancy: 27.5 % / Biso Wilson estimate: 62.24 Å2 / Rsym value: 0.406 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.6 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model based on 5JRT

5jrt


Resolution: 2.5→82.57 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.949 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.362 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.339 / SU Rfree Blow DPI: 0.213 / SU Rfree Cruickshank DPI: 0.22
RfactorNum. reflection% reflectionSelection details
Rfree0.211 802 4.86 %RANDOM
Rwork0.191 ---
obs0.192 16498 100 %-
Displacement parametersBiso mean: 65.21 Å2
Baniso -1Baniso -2Baniso -3
1--4.4085 Å20 Å21.2705 Å2
2--1.0037 Å20 Å2
3---3.4048 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→82.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 0 24 2879
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012891HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.133870HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1066SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes69HARMONIC2
X-RAY DIFFRACTIONt_gen_planes420HARMONIC5
X-RAY DIFFRACTIONt_it2891HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion19.82
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion375SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3196SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.247 143 4.86 %
Rwork0.22 2797 -
all0.222 2940 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.42642.9231-1.83816.8949-0.09946.9750.0337-0.0231-0.2164-0.00620.1205-0.2521-0.19620.5104-0.15420.0246-0.0276-0.0061-0.1470.0315-0.091118.270418.580233.3038
27.1628-0.98312.31444.0233-1.69728.82850.16360.51290.4138-0.5423-0.30990.06920.08040.31550.14620.07980.04010.0361-0.15630.1294-0.168718.7139-7.1684.531
36.97791.52771.45976.0869-2.48738.59090.00750.5239-0.3661-0.46640.1597-0.11670.52810.1819-0.16710.0835-0.03590.0729-0.2092-0.0927-0.170927.3306-21.783519.6748
40.44520.75860.46045.6473-1.12197.82310.07070.1475-0.01630.1971-0.19080.15720.1434-0.01350.120.0838-0.02950.0144-0.18-0.0402-0.06174.88320.998422.8713
58.61221.4874-2.87795.2808-0.83397.6859-0.0401-0.5534-0.38620.0748-0.0054-0.53930.25350.26280.04550.023-0.0168-0.0291-0.1484-0.0369-0.1429-8.9544-12.384535.7627
66.4927-1.09941.70015.0335-0.27698.69-0.0915-0.05060.1794-0.1890.1588-0.1817-0.24020.0673-0.06740.0433-0.0508-0.0592-0.1864-0.0626-0.1169-2.764520.552611.4436
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }

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