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

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Basic information

Entry
Database: PDB / ID: 5jti
TitleCrystal structure of the human Tankyrase 1 (TNKS) SAM domain (D1055R), crystal form 2
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 / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / 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 / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / mitotic spindle pole / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / mRNA transport / spindle assembly / nuclear pore / positive regulation of telomerase activity / 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 / positive regulation of canonical Wnt signaling pathway / protein transport / 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 / cytosol / cytoplasm
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: 2.9 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 9, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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
Water1,11762
1
A: Tankyrase-1


Theoretical massNumber of molelcules
Total (without water)8,8541
Polymers8,8541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tankyrase-1


Theoretical massNumber of molelcules
Total (without water)8,8541
Polymers8,8541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tankyrase-1


Theoretical massNumber of molelcules
Total (without water)8,8541
Polymers8,8541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tankyrase-1


Theoretical massNumber of molelcules
Total (without water)8,8541
Polymers8,8541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Tankyrase-1


Theoretical massNumber of molelcules
Total (without water)8,8541
Polymers8,8541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Tankyrase-1


Theoretical massNumber of molelcules
Total (without water)8,8541
Polymers8,8541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.934, 55.480, 79.414
Angle α, β, γ (deg.)90.00, 102.90, 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 / Plasmid: shuttle vector pPpT4 / Production host: Escherichia coli (E. coli) / References: UniProt: O95271, NAD+ ADP-ribosyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 3.61 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris pH 5.5 0.2 M Magnesium Chloride 25% PEG 3350

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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: 2.9→77.41 Å / Num. obs: 15085 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 77.36 Å2 / Rmerge(I) obs: 0.229 / Net I/σ(I): 7.4
Reflection shellResolution: 2.9→3 Å

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Processing

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

5jrt


Resolution: 2.9→77.41 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.903 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.694 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.659 / SU Rfree Blow DPI: 0.304 / SU Rfree Cruickshank DPI: 0.312
RfactorNum. reflection% reflectionSelection details
Rfree0.232 681 5.01 %RANDOM
Rwork0.193 ---
obs0.195 13593 100 %-
Displacement parametersBiso mean: 53.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.1657 Å20 Å2-0.1949 Å2
2--0.5412 Å20 Å2
3---1.6245 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.9→77.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2854 0 0 62 2916
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012899HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.193884HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1076SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes421HARMONIC5
X-RAY DIFFRACTIONt_it2899HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.5
X-RAY DIFFRACTIONt_other_torsion20.11
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion378SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3316SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.13 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.289 140 5.06 %
Rwork0.257 2627 -
all0.259 2767 -
obs--99.96 %
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)
14.26482.2388-1.33384.67010.86055.2688-0.04730.41490.34450.4004-0.16790.60820.3018-0.22970.21530.0443-0.01510.0378-0.1147-0.0348-0.047-23.20017.7415-16.2667
28.20193.4867-0.90266.091-2.18726.0507-0.14910.05270.4602-0.42390.33970.2510.0760.2021-0.1905-0.07660.0543-0.0268-0.1013-0.021-0.0611-11.629924.3202-4.3205
36.9292-0.08770.75018.3154-1.51568.7317-0.00920.354-0.5803-0.2046-0.0741-0.1820.26090.48370.0833-0.07770.0380.038-0.1353-0.0942-0.0551-0.949541.3714-15.6215
49.5822-2.1023-2.62036.13590.90887.0487-0.0250.1243-0.51920.30840.23710.56130.2059-0.0699-0.2121-0.11090.08730.0738-0.18370.02670.029-31.921821.7935.5051
53.3056-0.58331.7635.5577-0.78869.38580.03130.41750.2531-0.5141-0.0648-0.1931-0.09030.57520.0336-0.0615-0.0743-0.0357-0.00790.051-0.0947-7.1104-0.276-32.5212
65.8269-2.41882.34058.3154-2.47559.5181-0.0553-0.17520.39980.31340.0704-0.1529-0.561-0.2848-0.01510.00760.0665-0.1385-0.1893-0.1037-0.1179-31.202826.7091-27.4786
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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