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- PDB-5jrt: Crystal structure of the human Tankyrase 2 (TNKS2) SAM domain (DH... -

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Basic information

Entry
Database: PDB / ID: 5jrt
TitleCrystal structure of the human Tankyrase 2 (TNKS2) SAM domain (DH902/924RE)
ComponentsTankyrase-2
KeywordsSIGNALING PROTEIN / Tankyrase polymerisation Wnt signalling Poly(ADP-ribose)polymerase (PARP) / Transferase / signalling protein
Function / homology
Function and homology information


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 / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity ...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 / positive regulation of telomere capping / NAD+-protein ADP-ribosyltransferase activity / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Transcription Factor, Ets-1 / : / Ankyrin repeat / 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. ...Transcription Factor, Ets-1 / : / Ankyrin repeat / 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-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsGuettler, S. / Mariotti, L. / Cronin, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
United Kingdom
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 6, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Source and taxonomy
Revision 1.2May 1, 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-2


Theoretical massNumber of molelcules
Total (without water)8,8011
Polymers8,8011
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.630, 56.630, 46.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Tankyrase-2 / TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / ...TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-like protein / Tankyrase-related protein


Mass: 8801.161 Da / Num. of mol.: 1 / Fragment: UNP residues 867-940
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNKS2, PARP5B, TANK2, TNKL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 285.15 K / Method: vapor diffusion, sitting drop
Details: PEG 3350 20% 0.1 MTris-HCl pH 8.5 0.2 M Ammonium Acetate

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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: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.53→49.05 Å / Num. obs: 12770 / % possible obs: 100 % / Redundancy: 17 % / Biso Wilson estimate: 40.23 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 17
Reflection shellResolution: 1.53→1.58 Å / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1v85_A, 3bs5_B, 3bq_7, 2e8o_A, 2gle_A

Resolution: 1.53→28.32 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.947 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.075 / SU Rfree Cruickshank DPI: 0.074
RfactorNum. reflection% reflectionSelection details
Rfree0.235 636 4.98 %RANDOM
Rwork0.201 ---
obs0.203 12770 100 %-
Displacement parametersBiso mean: 46.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.9682 Å20 Å20 Å2
2--0.9682 Å20 Å2
3----1.9365 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.53→28.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms510 0 0 40 550
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01516HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.94690HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d194SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes13HARMONIC2
X-RAY DIFFRACTIONt_gen_planes75HARMONIC5
X-RAY DIFFRACTIONt_it516HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion15.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion67SEMIHARMONIC5
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_contact616SEMIHARMONIC4
LS refinement shellResolution: 1.53→1.68 Å / Rfactor Rfree error: 0 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.246 158 5.24 %
Rwork0.227 2856 -
all0.228 3014 -
obs--100 %
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)
15.1597-1.6682-1.64851.7115-2.96552.949-0.06550.0171-0.0465-0.08610.09610.4336-0.0958-0.6838-0.0306-0.10680.00090.001-0.0121-0.0483-0.024226.65816.75932.0556
2-0.46750.7619-0.54764.53111.6257.8024-0.2573-0.1661-0.18590.5046-0.09420.36310-0.0660.35140.052-0.04390.08910.0563-0.05280.043332.68153.68468.9467
33.0472-0.99940.63768.88671.19978.0145-0.003-0.0759-0.0861-0.46560.1178-0.6781-0.08170.5313-0.1149-0.0348-0.06820.0616-0.0147-0.07350.052539.54937.79440.4931
43.0511-0.51441.56357.4447-2.05184.3622-0.0010.15670.0392-0.67820.1013-0.09990.30430.0307-0.10030.0235-0.00880.0396-0.1098-0.0651-0.057935.24860.6107-4.4816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|874 - A|887 }
2X-RAY DIFFRACTION2{ A|888 - A|896 }
3X-RAY DIFFRACTION3{ A|897 - A|914 }
4X-RAY DIFFRACTION4{ A|915 - A|937 }

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