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

ID or keywords:

Entry

Database: PDB / ID: 4tor

Title

Crystal structure of Tankyrase 1 with IWR-8

Components

Tankyrase-1

Keywords

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.501 Å

Authors

Chen, H. / Zhang, X. / Lum, L. / Chen, C.

Funding support

United States, 2items

Citation

Journal: 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

Deposition	Jun 6, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 20, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jul 1, 2015	Group: Database references
Revision 1.2	Sep 20, 2017	Group: 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 1.3	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4tor.cif.gz	510.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4tor.ent.gz	427.1 KB	Display	PDB format
PDBx/mmJSON format	4tor.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4tor_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	4tor_full_validation.pdf.gz	1.9 MB	Display
Data in XML	4tor_validation.xml.gz	45.1 KB	Display
Data in CIF	4tor_validation.cif.gz	62.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/to/4tor ftp://data.pdbj.org/pub/pdb/validation_reports/to/4tor	HTTPS FTP

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Related structure data

Related structure data	4oa7C 4tosC 3kr8S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4pnm-2 6tkq-1 4pns-3 5ebt-1 4uw1-2 4dvi-1 3mhj-2 6tkp-1 7kkq-2 5nvc-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4oa7C

4tosC

3kr8S

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#250 - Oct 2020 Capsaicin Receptor TRPV1 similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Tankyrase-1

B: Tankyrase-1

C: Tankyrase-1

D: Tankyrase-1

hetero molecules

111 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Tankyrase-1

hetero molecules

defined by author
27.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Tankyrase-1

hetero molecules

defined by author
27.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Tankyrase-1

hetero molecules

defined by author
27.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Tankyrase-1

hetero molecules

defined by author
27.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

A: Tankyrase-1

hetero molecules

A: Tankyrase-1

hetero molecules

defined by software
55.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

B: Tankyrase-1

hetero molecules

B: Tankyrase-1

hetero molecules

defined by software
55.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

C: Tankyrase-1

hetero molecules

C: Tankyrase-1

hetero molecules

defined by software
55.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

D: Tankyrase-1

hetero molecules

D: Tankyrase-1

hetero molecules

defined by software
55.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	171
Space group name H-M	P6₂

Components on special symmetry positions

ID	Model	Components
1	1	A-1549- HOH
2	1	B-1562- HOH
3	1	B-1580- HOH
4	1	C-1570- HOH
5	1	C-1573- HOH
6	1	C-1585- HOH
7	1	D-1577- HOH
8	1	D-1581- HOH

#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 Mass: 35.453 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 824 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 1.93 Å³/Da / Density % sol: 36.2 %
Crystal grow	Temperature: 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

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

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
PHENIX	(phenix.refine: 1.8.4_1496)	refinement

Refinement

Method 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2068	6408	5 %	Random selection
R_work	0.1772	-	-	-
obs	0.1786	128274	99 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.501→37.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6712	0	163	824	7699

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7121
X-RAY DIFFRACTION	f_angle_d	1.072	9617
X-RAY DIFFRACTION	f_dihedral_angle_d	17.62	2645
X-RAY DIFFRACTION	f_chiral_restr	0.045	942
X-RAY DIFFRACTION	f_plane_restr	0.006	1267

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.501-1.5178	0.3096	190	0.3078	3606	X-RAY DIFFRACTION	89
1.5178-1.5357	0.2881	203	0.2926	3755	X-RAY DIFFRACTION	92
1.5357-1.5544	0.3169	204	0.2816	3919	X-RAY DIFFRACTION	95
1.5544-1.5741	0.2937	208	0.2666	4020	X-RAY DIFFRACTION	98
1.5741-1.5948	0.2891	217	0.2527	4051	X-RAY DIFFRACTION	100
1.5948-1.6166	0.2582	217	0.2418	4098	X-RAY DIFFRACTION	100
1.6166-1.6397	0.2491	209	0.2335	4068	X-RAY DIFFRACTION	100
1.6397-1.6642	0.2451	215	0.2219	4085	X-RAY DIFFRACTION	100
1.6642-1.6902	0.2499	217	0.2111	4071	X-RAY DIFFRACTION	100
1.6902-1.7179	0.2556	219	0.2121	4119	X-RAY DIFFRACTION	100
1.7179-1.7475	0.2184	215	0.1995	4064	X-RAY DIFFRACTION	100
1.7475-1.7793	0.2143	216	0.2	4137	X-RAY DIFFRACTION	100
1.7793-1.8135	0.2012	210	0.1924	4080	X-RAY DIFFRACTION	100
1.8135-1.8506	0.2251	217	0.1877	4063	X-RAY DIFFRACTION	100
1.8506-1.8908	0.2063	214	0.1858	4079	X-RAY DIFFRACTION	100
1.8908-1.9348	0.2176	226	0.1773	4127	X-RAY DIFFRACTION	100
1.9348-1.9832	0.2261	209	0.1826	4091	X-RAY DIFFRACTION	100
1.9832-2.0368	0.212	217	0.1736	4111	X-RAY DIFFRACTION	100
2.0368-2.0967	0.2314	223	0.1728	4062	X-RAY DIFFRACTION	100
2.0967-2.1644	0.2192	216	0.1684	4105	X-RAY DIFFRACTION	100
2.1644-2.2417	0.198	213	0.169	4101	X-RAY DIFFRACTION	100
2.2417-2.3315	0.2066	205	0.1677	4091	X-RAY DIFFRACTION	100
2.3315-2.4376	0.2081	217	0.165	4130	X-RAY DIFFRACTION	100
2.4376-2.566	0.1968	214	0.1666	4092	X-RAY DIFFRACTION	100
2.566-2.7268	0.2036	219	0.165	4120	X-RAY DIFFRACTION	100
2.7268-2.9372	0.1725	210	0.1638	4101	X-RAY DIFFRACTION	100
2.9372-3.2327	0.1767	220	0.159	4104	X-RAY DIFFRACTION	100
3.2327-3.7001	0.1772	216	0.1533	4119	X-RAY DIFFRACTION	100
3.7001-4.6603	0.1773	214	0.1374	4136	X-RAY DIFFRACTION	100
4.6603-37.3818	0.2037	218	0.1913	4161	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.379	0.4929	-0.5009	1.1322	0.0272	3.106	-0.0082	0.1732	0.0627	-0.0884	0.0097	0.1042	0.122	-0.3961	0.004	0.1094	0.0025	-0.0155	0.113	0.023	0.1772	-95.229	130.2881	-2.5185
2	3.0543	-1.5205	-1.3842	3.3998	0.2725	1.4866	0.1089	0.2234	0.046	-0.3735	-0.0849	-0.2947	0.0484	0.0131	-0.0326	0.1329	-0.0352	-0.0395	0.1596	-0.0082	0.1247	-80.1087	124.2264	-11.6215
3	0.9314	-0.4851	-0.5301	1.6229	0.5669	1.0219	0.0006	-0.0136	-0.1244	-0.0164	-0.0198	0.0551	0.0475	0.0106	0.0157	0.1041	-0.0087	-0.0189	0.1271	0.0149	0.1345	-82.9549	127.5381	1.7598
4	2.0728	-1.0586	-0.0007	2.3802	-0.0977	0.6057	-0.0999	-0.2169	-0.211	0.1799	0.0799	0.0844	0.1	-0.0074	0.0347	0.1278	-0.0116	-0.007	0.1483	0.0081	0.1542	-83.1587	118.2429	2.7087
5	4.3625	0.3065	0.915	1.4219	0.3168	2.0034	-0.073	0.6214	-0.2479	-0.2165	0.1122	-0.1604	-0.1049	0.2847	-0.0374	0.1711	-0.0221	0.0226	0.2046	-0.042	0.1582	-41.5508	102.711	-10.973
6	2.4887	0.2092	1.5325	1.3362	-0.0417	3.2547	-0.0053	-0.0403	-0.0902	0.0491	-0.0039	-0.125	-0.0928	0.2513	-0.0208	0.0904	-0.0197	0.0114	0.1044	-0.0155	0.1657	-41.4441	103.6896	2.539
7	4.2306	-0.4066	0.1987	9.0059	4.3225	4.5928	-0.0665	0.3008	0.2084	-0.4966	-0.0971	0.5346	-0.1342	-0.0258	0.1657	0.1684	-0.0099	-0.0392	0.2093	0.0319	0.1635	-61.0893	117.0682	-13.483
8	1.5536	-0.6254	0.4551	2.3739	-0.3742	0.944	-0.0507	-0.0511	0.0787	-0.0305	0.0341	-0.0247	-0.0367	-0.0331	0.0111	0.1	0.0017	0.0036	0.1253	-0.0124	0.1119	-55.0907	111.9922	-0.1366
9	4.2737	-1.7385	0.4638	8.0397	1.6086	4.1125	-0.0026	-0.2079	-0.0877	0.1332	-0.1052	0.1946	0.1312	-0.0661	0.076	0.1426	-0.0265	0.0111	0.1768	-0.0132	0.1142	-49.4554	95.8928	11.958
10	1.2988	-0.8243	0.3653	1.6386	-0.5788	0.6148	-0.0912	-0.1633	0.1929	0.1785	0.0729	-0.1217	-0.1034	-0.0181	0.024	0.1457	-0.0094	-0.0146	0.155	-0.0203	0.1531	-51.5805	116.0782	4.4434
11	3.1758	-2.2168	0.0323	3.671	-0.2582	1.0316	-0.0369	0.0059	0.0416	0.027	0.01	-0.0504	-0.0348	-0.0148	0.0334	0.0797	-0.0344	0.0034	0.1007	-0.005	0.1042	-50.1308	107.6716	-1.7074
12	1.6018	0.6635	-0.3733	1.2421	-0.3493	3.3719	0.0216	-0.0729	0.0723	0.0669	-0.0378	-0.0011	-0.2264	0.2372	0.0183	0.1496	0.0009	0.0212	0.1349	-0.0134	0.265	-92.4005	100.4991	-3.353
13	2.024	-0.9699	-0.4469	4.4678	-1.336	1.5295	-0.0901	-0.2634	-0.1448	0.3638	0.1003	0.2302	0.0057	0.0449	-0.0134	0.12	-0.0327	-0.0268	0.1705	-0.0338	0.1543	-94.6407	84.6483	5.7826
14	0.8294	-0.685	0.2399	1.6235	-0.8287	1.0717	-0.0219	-0.0218	0.03	0.0011	0.0033	-0.104	0.0217	0.0151	0.0078	0.1195	-0.014	0.0093	0.1231	-0.0179	0.1819	-96.1149	88.6753	-7.6123
15	1.1051	-0.2869	0.0154	2.5666	0.1902	0.5594	0.0164	0.0998	0.0434	-0.2383	-0.0028	-0.114	0.0041	0.0757	-0.0093	0.1088	-0.0145	0.0134	0.123	0.0056	0.1426	-87.8739	84.1929	-8.4653
16	0.853	-0.2746	-0.4714	2.2837	0.2241	3.192	-0.0443	-0.0553	-0.0173	0.1196	0.017	-0.0581	0.3633	0.0633	0.0536	0.1174	-0.001	-0.0313	0.1252	-0.0031	0.2088	-83.4192	123.5039	37.3379
17	4.0714	-0.642	-0.7324	1.729	1.1215	1.3776	0.0263	-0.3176	0.2253	0.1662	-0.007	0.016	0.012	-0.0347	-0.0233	0.1869	-0.0136	-0.0145	0.1041	0.0518	0.1482	-96.1791	133.5293	46.5072
18	2.0191	0.0186	-0.8008	0.3935	0.1394	1.0445	0.0157	0.0175	-0.1238	-0.0161	-0.0095	0.0636	-0.0173	-0.0468	-0.0098	0.1369	0.0063	-0.0263	0.1057	0.0045	0.1573	-91.9425	132.7347	33.105
19	3.0415	-0.441	0.1986	0.9202	-0.0491	0.5386	0.0769	0.2772	-0.1602	-0.1195	-0.0623	0.0858	0.0666	-0.0768	-0.0161	0.164	0.0028	-0.0059	0.1319	-0.0017	0.174	-99.9004	127.9318	32.1847

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1105 through 1144 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1145 through 1172 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1173 through 1255 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1256 through 1313 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1105 through 1127 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1128 through 1155 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1156 through 1172 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1173 through 1224 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1225 through 1240 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1241 through 1290 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 1291 through 1313 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1105 through 1144 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1145 through 1172 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1173 through 1255 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1256 through 1313 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1105 through 1144 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1145 through 1172 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 1173 through 1255 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1256 through 1313 )

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About Yorodumi

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Yorodumi