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- PDB-4tor: Crystal structure of Tankyrase 1 with IWR-8 -

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Basic information

Entry
Database: PDB / ID: 4tor
TitleCrystal structure of Tankyrase 1 with IWR-8
ComponentsTankyrase-1
KeywordsTRANSFERASE
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
Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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 ...Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-IW8 / Poly [ADP-ribose] polymerase tankyrase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å
AuthorsChen, H. / Zhang, X. / Lum, L. / Chen, C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM088197 United States
Welch FoundationI-1702 United States
CitationJournal: Mol.Cell.Biol. / Year: 2015
Title: Disruption of Wnt/ beta-Catenin Signaling and Telomeric Shortening Are Inextricable Consequences of Tankyrase Inhibition in Human Cells.
Authors: Kulak, O. / Chen, H. / Holohan, B. / Wu, X. / He, H. / Borek, D. / Otwinowski, Z. / Yamaguchi, K. / Garofalo, L.A. / Ma, Z. / Wright, W. / Chen, C. / Shay, J.W. / Zhang, X. / Lum, L.
History
DepositionJun 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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 / refine_hist
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,74935
Polymers107,4864
Non-polymers3,26331
Water14,844824
1
A: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6618
Polymers26,8711
Non-polymers7897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6969
Polymers26,8711
Non-polymers8258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6969
Polymers26,8711
Non-polymers8258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6969
Polymers26,8711
Non-polymers8258
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Tankyrase-1
hetero molecules

A: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,32116
Polymers53,7432
Non-polymers1,57814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_585-x,-y+3,z1
Buried area3200 Å2
ΔGint-111 kcal/mol
Surface area19230 Å2
MethodPISA
6
B: Tankyrase-1
hetero molecules

B: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,39218
Polymers53,7432
Non-polymers1,64916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575-x,-y+2,z1
Buried area3530 Å2
ΔGint-134 kcal/mol
Surface area18870 Å2
MethodPISA
7
C: Tankyrase-1
hetero molecules

C: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,39218
Polymers53,7432
Non-polymers1,64916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_475-x-1,-y+2,z1
Buried area3280 Å2
ΔGint-117 kcal/mol
Surface area19030 Å2
MethodPISA
8
D: Tankyrase-1
hetero molecules

D: Tankyrase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,39218
Polymers53,7432
Non-polymers1,64916
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_585-x,-y+3,z1
Buried area3760 Å2
ΔGint-151 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.382, 108.382, 122.215
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-1549-

HOH

21B-1562-

HOH

31B-1580-

HOH

41C-1570-

HOH

51C-1573-

HOH

61C-1585-

HOH

71D-1577-

HOH

81D-1581-

HOH

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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: 26871.389 Da / Num. of mol.: 4 / Fragment: UNP residues 1105-1315 / Mutation: M1266I
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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IW8 / 1-[(1-acetyl-5-bromo-1H-indol-6-yl)sulfonyl]-N-ethyl-N-(3-methylphenyl)piperidine-4-carboxamide


Mass: 546.477 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H28BrN3O4S
#4: Chemical...
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 824 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.93 Å3/Da / Density % sol: 36.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Bis-Tris propane, 0.2M sodium bromide, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791516 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791516 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 129625 / Num. obs: 128452 / % possible obs: 99.1 % / Redundancy: 6.2 % / Rsym value: 0.083 / Net I/σ(I): 26.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.3 / % possible all: 89.3

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KR8

3kr8


Resolution: 1.501→37.37 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / Phase error: 22.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 6408 5 %Random selection
Rwork0.1772 ---
obs0.1786 128274 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.501→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6712 0 163 824 7699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077121
X-RAY DIFFRACTIONf_angle_d1.0729617
X-RAY DIFFRACTIONf_dihedral_angle_d17.622645
X-RAY DIFFRACTIONf_chiral_restr0.045942
X-RAY DIFFRACTIONf_plane_restr0.0061267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.501-1.51780.30961900.30783606X-RAY DIFFRACTION89
1.5178-1.53570.28812030.29263755X-RAY DIFFRACTION92
1.5357-1.55440.31692040.28163919X-RAY DIFFRACTION95
1.5544-1.57410.29372080.26664020X-RAY DIFFRACTION98
1.5741-1.59480.28912170.25274051X-RAY DIFFRACTION100
1.5948-1.61660.25822170.24184098X-RAY DIFFRACTION100
1.6166-1.63970.24912090.23354068X-RAY DIFFRACTION100
1.6397-1.66420.24512150.22194085X-RAY DIFFRACTION100
1.6642-1.69020.24992170.21114071X-RAY DIFFRACTION100
1.6902-1.71790.25562190.21214119X-RAY DIFFRACTION100
1.7179-1.74750.21842150.19954064X-RAY DIFFRACTION100
1.7475-1.77930.21432160.24137X-RAY DIFFRACTION100
1.7793-1.81350.20122100.19244080X-RAY DIFFRACTION100
1.8135-1.85060.22512170.18774063X-RAY DIFFRACTION100
1.8506-1.89080.20632140.18584079X-RAY DIFFRACTION100
1.8908-1.93480.21762260.17734127X-RAY DIFFRACTION100
1.9348-1.98320.22612090.18264091X-RAY DIFFRACTION100
1.9832-2.03680.2122170.17364111X-RAY DIFFRACTION100
2.0368-2.09670.23142230.17284062X-RAY DIFFRACTION100
2.0967-2.16440.21922160.16844105X-RAY DIFFRACTION100
2.1644-2.24170.1982130.1694101X-RAY DIFFRACTION100
2.2417-2.33150.20662050.16774091X-RAY DIFFRACTION100
2.3315-2.43760.20812170.1654130X-RAY DIFFRACTION100
2.4376-2.5660.19682140.16664092X-RAY DIFFRACTION100
2.566-2.72680.20362190.1654120X-RAY DIFFRACTION100
2.7268-2.93720.17252100.16384101X-RAY DIFFRACTION100
2.9372-3.23270.17672200.1594104X-RAY DIFFRACTION100
3.2327-3.70010.17722160.15334119X-RAY DIFFRACTION100
3.7001-4.66030.17732140.13744136X-RAY DIFFRACTION100
4.6603-37.38180.20372180.19134161X-RAY DIFFRACTION99
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)
12.3790.4929-0.50091.13220.02723.106-0.00820.17320.0627-0.08840.00970.10420.122-0.39610.0040.10940.0025-0.01550.1130.0230.1772-95.229130.2881-2.5185
23.0543-1.5205-1.38423.39980.27251.48660.10890.22340.046-0.3735-0.0849-0.29470.04840.0131-0.03260.1329-0.0352-0.03950.1596-0.00820.1247-80.1087124.2264-11.6215
30.9314-0.4851-0.53011.62290.56691.02190.0006-0.0136-0.1244-0.0164-0.01980.05510.04750.01060.01570.1041-0.0087-0.01890.12710.01490.1345-82.9549127.53811.7598
42.0728-1.0586-0.00072.3802-0.09770.6057-0.0999-0.2169-0.2110.17990.07990.08440.1-0.00740.03470.1278-0.0116-0.0070.14830.00810.1542-83.1587118.24292.7087
54.36250.30650.9151.42190.31682.0034-0.0730.6214-0.2479-0.21650.1122-0.1604-0.10490.2847-0.03740.1711-0.02210.02260.2046-0.0420.1582-41.5508102.711-10.973
62.48870.20921.53251.3362-0.04173.2547-0.0053-0.0403-0.09020.0491-0.0039-0.125-0.09280.2513-0.02080.0904-0.01970.01140.1044-0.01550.1657-41.4441103.68962.539
74.2306-0.40660.19879.00594.32254.5928-0.06650.30080.2084-0.4966-0.09710.5346-0.1342-0.02580.16570.1684-0.0099-0.03920.20930.03190.1635-61.0893117.0682-13.483
81.5536-0.62540.45512.3739-0.37420.944-0.0507-0.05110.0787-0.03050.0341-0.0247-0.0367-0.03310.01110.10.00170.00360.1253-0.01240.1119-55.0907111.9922-0.1366
94.2737-1.73850.46388.03971.60864.1125-0.0026-0.2079-0.08770.1332-0.10520.19460.1312-0.06610.0760.1426-0.02650.01110.1768-0.01320.1142-49.455495.892811.958
101.2988-0.82430.36531.6386-0.57880.6148-0.0912-0.16330.19290.17850.0729-0.1217-0.1034-0.01810.0240.1457-0.0094-0.01460.155-0.02030.1531-51.5805116.07824.4434
113.1758-2.21680.03233.671-0.25821.0316-0.03690.00590.04160.0270.01-0.0504-0.0348-0.01480.03340.0797-0.03440.00340.1007-0.0050.1042-50.1308107.6716-1.7074
121.60180.6635-0.37331.2421-0.34933.37190.0216-0.07290.07230.0669-0.0378-0.0011-0.22640.23720.01830.14960.00090.02120.1349-0.01340.265-92.4005100.4991-3.353
132.024-0.9699-0.44694.4678-1.3361.5295-0.0901-0.2634-0.14480.36380.10030.23020.00570.0449-0.01340.12-0.0327-0.02680.1705-0.03380.1543-94.640784.64835.7826
140.8294-0.6850.23991.6235-0.82871.0717-0.0219-0.02180.030.00110.0033-0.1040.02170.01510.00780.1195-0.0140.00930.1231-0.01790.1819-96.114988.6753-7.6123
151.1051-0.28690.01542.56660.19020.55940.01640.09980.0434-0.2383-0.0028-0.1140.00410.0757-0.00930.1088-0.01450.01340.1230.00560.1426-87.873984.1929-8.4653
160.853-0.2746-0.47142.28370.22413.192-0.0443-0.0553-0.01730.11960.017-0.05810.36330.06330.05360.1174-0.001-0.03130.1252-0.00310.2088-83.4192123.503937.3379
174.0714-0.642-0.73241.7291.12151.37760.0263-0.31760.22530.1662-0.0070.0160.012-0.0347-0.02330.1869-0.0136-0.01450.10410.05180.1482-96.1791133.529346.5072
182.01910.0186-0.80080.39350.13941.04450.01570.0175-0.1238-0.0161-0.00950.0636-0.0173-0.0468-0.00980.13690.0063-0.02630.10570.00450.1573-91.9425132.734733.105
193.0415-0.4410.19860.9202-0.04910.53860.07690.2772-0.1602-0.1195-0.06230.08580.0666-0.0768-0.01610.1640.0028-0.00590.1319-0.00170.174-99.9004127.931832.1847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1105 through 1144 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1145 through 1172 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1173 through 1255 )
4X-RAY DIFFRACTION4chain 'A' and (resid 1256 through 1313 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1105 through 1127 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1128 through 1155 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1156 through 1172 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1173 through 1224 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1225 through 1240 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1241 through 1290 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1291 through 1313 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1105 through 1144 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1145 through 1172 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1173 through 1255 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1256 through 1313 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1105 through 1144 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1145 through 1172 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1173 through 1255 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1256 through 1313 )

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