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- PDB-4tkf: Crystal Structure of human Tankyrase 2 in complex with IWR-1. -

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Basic information

Entry
Database: PDB / ID: 4tkf
TitleCrystal Structure of human Tankyrase 2 in complex with IWR-1.
ComponentsTankyrase-2
KeywordsTRANSFERASE / poly(ADP-ribosylation) polymerase (PARP)
Function / homology
Function and homology information


XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein localization to chromosome, telomeric region / NAD+-protein-aspartate ADP-ribosyltransferase activity / protein poly-ADP-ribosylation / NAD+-protein-glutamate ADP-ribosyltransferase activity / NAD+-protein mono-ADP-ribosyltransferase activity / pericentriolar material / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ poly-ADP-ribosyltransferase activity / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Regulation of PTEN stability and activity / Wnt signaling pathway / 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 / metal ion binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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 ...Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-33C / 3-aminobenzamide / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsQiu, W. / Lam, R. / Romanov, V. / Gordon, R. / Gebremeskel, S. / Vodsedalek, J. / Thompson, C. / Beletskaya, I. / Battaile, K.P. / Pai, E.F. / Chirgadze, N.Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2.
Authors: Qiu, W. / Lam, R. / Voytyuk, O. / Romanov, V. / Gordon, R. / Gebremeskel, S. / Vodsedalek, J. / Thompson, C. / Beletskaya, I. / Battaile, K.P. / Pai, E.F. / Rottapel, R. / Chirgadze, N.Y.
History
DepositionMay 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2015Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.pdbx_keywords
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tankyrase-2
B: Tankyrase-2
C: Tankyrase-2
D: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,12514
Polymers103,9454
Non-polymers2,18010
Water5,693316
1
A: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5994
Polymers25,9861
Non-polymers6133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4633
Polymers25,9861
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5994
Polymers25,9861
Non-polymers6133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4633
Polymers25,9861
Non-polymers4772
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.360, 78.590, 151.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Details1

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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: 25986.291 Da / Num. of mol.: 4 / Fragment: PARP, catalytic domain
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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-33C / 4-[(3aR,4R,7S,7aS)-1,3-dioxooctahydro-2H-4,7-methanoisoindol-2-yl]-N-(quinolin-8-yl)benzamide


Mass: 411.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H21N3O3
#4: Chemical ChemComp-3AB / 3-aminobenzamide


Mass: 136.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.1 Å3/Da / Density % sol: 41.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M NaCl, 0.1M Sodium, Hepes buffer at pH7.5, 12-15% iso-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jul 27, 2010 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 35412 / % possible obs: 99.6 % / Redundancy: 7.18 % / Biso Wilson estimate: 52.67 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 14.53 / Num. measured all: 255295
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. possibleNum. unique obsNet I/σ(I) obs% possible all
2.4-2.4670.659196919352.6498.3
2.46-2.517.220.639192919272.7399.9
2.51-2.567.250.577179517953.17100
2.56-2.627.260.552196919693.34100
2.62-2.697.250.5206520653.77100
2.69-2.767.270.441190319024.3399.9
2.76-2.847.260.395196119595.0599.9
2.84-2.937.30.327191319136.14100
2.93-3.037.290.288187918786.8799.9
3.03-3.147.290.222178917889.2299.9
3.14-3.277.30.1711837183511.5899.9
3.27-3.427.290.1371797179614.499.9
3.42-3.617.250.1141885188317.6299.9
3.61-3.857.20.0931852185022.0999.9
3.85-4.157.20.0671786178427.6199.9
4.15-4.587.210.0511788178634.7799.9
4.58-5.257.160.0481779177735.1399.9
5.25-6.637.070.0571799179830.3199.9
6.63-19.66.310.0361872177242.6594.7

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Processing

Software
NameVersionClassification
XDS2005/3data reduction
BUSTER-TNTBUSTER 2.8.0refinement
PDB_EXTRACT3.14data extraction
BUSTER2.8.0refinement
XPREPdata reduction
RefinementResolution: 2.6→19.6 Å / Cor.coef. Fo:Fc: 0.9324 / Cor.coef. Fo:Fc free: 0.8684 / Cross valid method: THROUGHOUT / σ(F): 0
Details: LARGE DIFFERENCE BETWEEN THE REPORTED R_FREE (0.251) AND R_WORK(0.166)
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 1389 5.03 %RANDOM
Rwork0.1661 ---
obs0.1704 27589 99.6 %-
Displacement parametersBiso max: 184 Å2 / Biso mean: 40.21 Å2 / Biso min: 8.79 Å2
Baniso -1Baniso -2Baniso -3
1--8.4579 Å20 Å20 Å2
2---4.1227 Å20 Å2
3---12.5805 Å2
Refine analyzeLuzzati coordinate error obs: 0.254 Å
Refinement stepCycle: final / Resolution: 2.6→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6440 0 148 316 6904
Biso mean--50.65 40.1 -
Num. residues----799
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2315SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes149HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1025HARMONIC5
X-RAY DIFFRACTIONt_it6633HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion791SEMIHARMONIC5
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_contact7914SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6797HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9160HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion19.53
LS refinement shellResolution: 2.6→2.7 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3489 141 4.94 %
Rwork0.1956 2714 -
all0.2033 2855 -

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