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- PDB-5kni: Crystal Structure of the wild-type SAM domain of human Tankyrase-1 -

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Basic information

Entry
Database: PDB / ID: 5kni
TitleCrystal Structure of the wild-type SAM domain of human Tankyrase-1
ComponentsTankyrase-1
KeywordsTRANSFERASE / tankyrase / sterile alpha motif SAM domain / TNKS / TNKS1
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+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / 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 / peptidyl-threonine phosphorylation / Degradation of AXIN / 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 / Golgi membrane / cell division / Golgi apparatus / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Transcription Factor, Ets-1 / : / 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 / : / 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
AuthorsPascal, J.M. / McCauley, M. / Langelier, M.F. / Riccio, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM087282 United States
CitationJournal: Structure / Year: 2016
Title: Tankyrase Sterile alpha Motif Domain Polymerization Is Required for Its Role in Wnt Signaling.
Authors: Riccio, A.A. / McCauley, M. / Langelier, M.F. / Pascal, J.M.
History
DepositionJun 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Structure summary
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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
G: Tankyrase-1


Theoretical massNumber of molelcules
Total (without water)52,9737
Polymers52,9737
Non-polymers00
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-19 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.322, 55.101, 92.441
Angle α, β, γ (deg.)90.00, 115.88, 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: 7567.637 Da / Num. of mol.: 7 / Fragment: UNP residues 1026 to 1092
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.: 113 / 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: 3.78 Å3/Da / Density % sol: 67.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M magnesium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.03319 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 30719 / % possible obs: 98.4 % / Redundancy: 6.3 % / Net I/σ(I): 10.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3h8m

3h8m


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 14.247 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.182 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21218 1538 5 %RANDOM
Rwork0.16822 ---
obs0.17042 29169 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 65.966 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.95 Å2
2---0.95 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3441 0 0 113 3554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193492
X-RAY DIFFRACTIONr_bond_other_d0.0020.023511
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9754668
X-RAY DIFFRACTIONr_angle_other_deg1.06838070
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8265425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.94224.686175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88515703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7111522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023876
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02782
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_it4.9323.1441715
X-RAY DIFFRACTIONr_mcbond_other4.9293.1431714
X-RAY DIFFRACTIONr_mcangle_it6.2924.7012132
X-RAY DIFFRACTIONr_mcangle_other6.2934.7032133
X-RAY DIFFRACTIONr_scbond_it8.7333.9371777
X-RAY DIFFRACTIONr_scbond_other8.7313.9381778
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.8945.5812536
X-RAY DIFFRACTIONr_long_range_B_refined13.10725.4983848
X-RAY DIFFRACTIONr_long_range_B_other13.11825.253819
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 99 -
Rwork0.306 2118 -
obs--97.36 %
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)
16.2159-0.4105-1.76854.53551.91839.5025-0.0264-0.1555-0.49970.2008-0.0226-0.0150.86450.16040.0490.4444-0.01360.00490.38810.0620.1802-33.2586-36.8442-2.0684
24.80650.76341.48938.94044.50346.3415-0.0633-0.2337-0.29610.3785-0.25680.31290.8911-0.38070.32010.3266-0.07880.05140.44460.02160.2203-40.5208-26.720217.1281
35.46480.59561.31526.5423-1.38597.9953-0.1410.00460.25040.10270.02090.3686-0.045-0.31750.12010.0385-0.0399-0.04390.2627-0.01180.2722-36.1232-8.2930.5899
49.29050.06250.53875.0195-1.41567.0054-0.107-0.22050.61090.20830.15740.3537-0.3789-0.362-0.05040.0801-0.037-0.05650.2537-0.01170.3267-17.33524.202635.4279
56.6064-1.6580.16877.19741.13184.825-0.06790.03130.1697-0.20520.056-0.0648-0.0385-0.13890.01190.0121-0.0224-0.02220.21840.03940.14825.24331.871839.1152
65.7042-0.6213-0.51377.4737-2.01316.6771-0.0969-0.10440.35290.1116-0.0312-0.2302-0.32220.17230.12810.06640.0304-0.01020.18030.00020.157220.9032-13.199445.8721
74.38661.683-1.0045.4461-1.38769.88250.0698-0.0926-0.19990.2564-0.0632-0.49790.37320.6169-0.00660.22470.0437-0.01590.320.01450.165223.5108-30.833760.9451
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1029 - 1086
2X-RAY DIFFRACTION2B1029 - 1088
3X-RAY DIFFRACTION3C1026 - 1090
4X-RAY DIFFRACTION4D1028 - 1088
5X-RAY DIFFRACTION5E1029 - 1090
6X-RAY DIFFRACTION6F1028 - 1088
7X-RAY DIFFRACTION7G1027 - 1089

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