PDB-3tww: Crystal structure of ARC4 from human Tankyrase 2 in complex with ...

ID or keywords:

Entry

Database: PDB / ID: 3tww

Title

Crystal structure of ARC4 from human Tankyrase 2 in complex with peptide from human LNPEP (chimeric peptide)

Components

Tankyrase-2
human LNPEP

Keywords

SIGNALING PROTEIN/PEPTIDE / ankyrin repeat / protein-protein interaction / substrate recruitment / poly(ADP-ribosyl)ation / SIGNALING PROTEIN-PEPTIDE complex

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Guettler, S. / Sicheri, F.

Citation

Journal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural basis and sequence rules for substrate recognition by tankyrase explain the basis for cherubism disease.
Authors: Guettler, S. / Larose, J. / Petsalaki, E. / Gish, G. / Scotter, A. / Pawson, T. / Rottapel, R. / Sicheri, F.

History

Deposition	Sep 22, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 7, 2011	Provider: repository / Type: Initial release
Revision 1.1	Dec 28, 2011	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3tww.cif.gz	143.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3tww.ent.gz	121.5 KB	Display	PDB format
PDBx/mmJSON format	3tww.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tw/3tww ftp://data.pdbj.org/pub/pdb/validation_reports/tw/3tww	HTTPS FTP

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Related structure data

Related structure data	3twqC 3twrC 3twsC 3twtC 3twuC 3twvC 3twxC C: citing same article (ref.)
Similar structure data	1nwk-d 1ijd-d 4v0u-6 5dcq-1 3twx-d 2p02-d 6ipp-d 3tz2-d 4k43-2 1gkx-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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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-2

B: Tankyrase-2

C: human LNPEP

D: human LNPEP

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	44.360, 74.191, 103.499
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Tankyrase-2 / TANK2 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose ...TANK2 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-like protein / Tankyrase-related protein Mass: 17851.180 Da / Num. of mol.: 2 / Fragment: UNP residues 488-649 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARP5B, TANK2, TNKL, TNKS2 / Plasmid: pETM-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Protein/peptide	human LNPEP Mass: 1855.043 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: solid-state synthesized peptide / Source: (synth.) Homo sapiens (human)
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.09 Å³/Da / Density % sol: 41.26 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M NaOAc pH 5.5, 2% (v/v) PEG 400, 2.5 M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2010
Radiation	Monochromator: Si (220), Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2→50 Å / Num. all: 23309 / Num. obs: 23309 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.7 / Redundancy: 5.8 % / R_merge(I) obs: 0.107 / Net I/σ(I): 14.7
Reflection shell	Resolution: 2→2.07 Å / Redundancy: 6 % / R_merge(I) obs: 0.599 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.7.1_743)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→35.732 Å / SU ML: 0.63 / σ(F): 0.49 / Phase error: 27.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2679	1192	5.13 %	Random
R_work	0.2182	-	-	-
obs	0.2209	23224	97.6 %	-
all	-	23224	-	-

Solvent computation

Shrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 50.825 Å² / k_sol: 0.351 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.8711 Å²	0 Å²	-0 Å²
2-	-	0.1207 Å²	0 Å²
3-	-	-	-3.9918 Å²

Refinement step

Cycle: LAST / Resolution: 2→35.732 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2594	0	10	143	2747

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	2668
X-RAY DIFFRACTION	f_angle_d	1.051	3610
X-RAY DIFFRACTION	f_dihedral_angle_d	15.512	988
X-RAY DIFFRACTION	f_chiral_restr	0.073	399
X-RAY DIFFRACTION	f_plane_restr	0.005	479

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 (%)
2-2.0801	0.3505	117	0.2851	2472	X-RAY DIFFRACTION	100
2.0801-2.1748	0.3478	144	0.2578	2438	X-RAY DIFFRACTION	99
2.1748-2.2894	0.3316	127	0.2331	2455	X-RAY DIFFRACTION	99
2.2894-2.4328	0.2774	130	0.2178	2455	X-RAY DIFFRACTION	100
2.4328-2.6206	0.2749	136	0.1949	2495	X-RAY DIFFRACTION	99
2.6206-2.8842	0.2649	118	0.2149	2478	X-RAY DIFFRACTION	99
2.8842-3.3013	0.2526	135	0.2006	2459	X-RAY DIFFRACTION	98
3.3013-4.1583	0.2459	158	0.1904	2315	X-RAY DIFFRACTION	92
4.1583-35.738	0.2536	127	0.2365	2465	X-RAY DIFFRACTION	92

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	5.6994	-1.9733	0.0931	3.5299	-3.1197	4.067	-0.2558	0.1688	-0.7702	-0.1794	0.1215	0.5092	1.0758	-0.6187	-0.0302	0.2403	-0.0889	0.016	0.2208	-0.0551	0.372	-15.1111	-12.5344	-0.9688
2	6.962	0.1812	-2.3973	2.3773	-0.0018	3.5695	-0.0842	0.4412	0.2016	-0.28	0.1404	0.7413	0.0828	-1.1598	-0.0467	0.1761	-0.0583	-0.1034	0.4002	-0.0487	0.5304	-21.5076	-4.9933	-5.3373
3	4.251	-0.2758	-1.6877	1.797	-0.7226	5.0246	-0.031	-0.5146	0.0347	0.1511	-0.0566	0.5177	0.3011	-0.1094	0.046	0.0892	-0.0351	-0.0143	0.1976	-0.0144	0.2512	-9.9076	-6.5022	1.8225
4	7.2848	-0.9779	-5.5559	1.6035	1.525	4.6494	0.079	0.0779	0.7674	-0.0916	-0.0657	0.3459	-0.3944	-0.7208	-0.187	0.0796	0.0433	-0.0768	0.3327	-0.0256	0.4502	-16.1442	3.5235	-2.7152
5	7.314	-0.699	0.2183	3.8059	-0.7245	6.2932	0.1423	-0.6066	-0.2723	0.1363	-0.0513	0.2197	0.2216	0.235	-0.0067	0.1247	0.0084	-0.0201	0.2841	-0.0017	0.2225	-3.7944	-1.3026	6.0211
6	6.7015	0.5376	0.1501	2.9891	2.1165	7.7225	-0.1707	0.2564	0.4361	-0.0323	-0.0227	0.0158	-0.3227	0.1003	0.1171	0.1141	-0.015	-0.0228	0.1995	0.0332	0.2305	-3.1836	4.9752	-5.0547
7	6.606	-0.6943	0.3725	3.0262	-0.185	2.1545	0.0607	-0.5276	0.5373	0.1292	-0.1348	-0.0623	-0.1648	0.0782	0.0862	0.0768	-0.0204	-0.0323	0.3122	-0.0512	0.2339	3.8694	3.1643	4.9573
8	7.1002	-0.5143	1.8446	1.8746	1.9494	4.4776	-0.297	0.6002	-0.0459	-0.1174	0.2079	0.0674	0.0355	0.207	-0.0583	0.1431	-0.0193	-0.0509	0.4104	0.0124	0.2906	7.8881	3.1543	-5.4358
9	3.005	1.4805	1.2539	1.6773	0.5013	1.7826	-0.428	0.5758	1.3796	-0.286	0.0491	0.2433	-0.5146	0.1576	0.2353	0.1948	-0.1433	-0.17	0.3405	0.2284	0.6743	3.9256	12.7992	-6.6914
10	7.4299	-5.3897	1.1467	7.3778	-0.0628	2.7867	-0.5236	-0.9232	0.6405	0.395	0.1632	0.1728	-0.2295	0.2835	0.2185	0.1712	-0.0371	-0.0927	0.4856	-0.0027	0.419	13.887	5.6451	4.1276
11	3.4147	0.8567	1.0502	1.958	0.0071	2.4421	-0.3264	1.1278	0.5007	-0.4291	0.4107	-0.0312	-0.2144	0.4524	0.0453	0.1797	-0.1888	-0.0428	0.754	0.1455	0.3238	15.7264	8.0595	-9.0113
12	7.037	-2.3622	4.9507	2.7221	-2.2535	3.6666	-0.2851	-0.277	0.4137	-0.0157	0.0706	0.6306	-0.7509	-1.732	0.1519	0.3585	0.0243	-0.0498	0.5759	0.0213	0.4006	-25.3795	2.8835	-30.4976
13	4.7789	0.9489	2.3861	3.5765	1.715	5.0884	-0.0473	-0.1404	0.2525	0.1104	-0.2048	0.3036	-0.0112	-0.8032	0.1192	0.2253	-0.0481	-0.0587	0.3121	-0.0098	0.2059	-18.0137	1.5513	-29.8633
14	3.7841	2.5706	-1.296	5.6943	-0.1896	5.4067	-0.1711	-0.0739	-0.132	-0.2086	-0.0839	-0.0665	0.0054	-0.0023	0.1934	0.1852	-0.0164	-0.1038	0.1912	-0.0095	0.1865	-10.3879	0.9458	-31.7026
15	2.1372	2.253	-0.6527	2.7668	0.7728	5.7829	-0.1913	0.0078	0.0735	0.1628	0.0965	-0.1869	-0.4227	0.14	0.063	0.2754	-0.0465	-0.0805	0.1199	0.0084	0.222	-3.8383	5.3474	-24.9248
16	2.6827	0.8569	-0.6343	2.5882	1.9769	2.5903	0.1068	0.1635	0.2191	-0.1245	-0.1256	-0.7659	-0.5971	0.397	-0.0164	0.4397	-0.0971	-0.1064	0.3157	0.0486	0.2489	-2.2172	12.0663	-35.0343
17	2.456	0.4393	-0.1622	2.4919	-0.8912	2.7837	0.1965	0.0769	-0.2729	0.3811	-0.1676	-0.6228	-0.548	0.426	0.1748	0.4467	-0.2085	-0.227	0.3235	0.1725	0.4938	3.481	15.1546	-27.5045
18	0.8255	0.5257	-0.2465	1.6395	-0.6358	0.9732	0.121	-0.136	-0.038	0.3508	-0.1203	-0.0999	-0.1427	0.0811	-0.0331	0.8058	-0.3814	-0.2941	0.3481	0.2998	0.5258	6.2741	21.5025	-20.9089
19	2.7869	0.2112	0.9998	0.8525	0.6765	1.708	0.0731	-0.2406	-0.2497	-0.1464	0.0802	-0.1892	0.2558	0.4307	-0.046	0.2184	0.0585	0.0511	0.316	0.0077	0.2626	1.0244	-6.5595	-7.5084
20	1.1957	0.2392	-0.1684	0.855	0.0508	0.8865	-0.0509	-0.0715	0.2096	0.0064	0.2561	0.0872	-0.2471	-0.0945	-0.1471	0.3916	0.0646	-0.1313	0.31	-0.0419	0.3243	-12.3661	13.2025	-21.7287

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 488:502)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 503:511)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 512:538)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 539:548)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 549:561)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 562:580)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 581:594)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 595:604)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 605:614)
10	X-RAY DIFFRACTION	10	chain 'A' and (resseq 615:627)
11	X-RAY DIFFRACTION	11	chain 'A' and (resseq 628:644)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 487:502)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 503:538)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 539:561)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 562:580)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 581:594)
17	X-RAY DIFFRACTION	17	chain 'B' and (resseq 595:627)
18	X-RAY DIFFRACTION	18	chain 'B' and (resseq 628:643)
19	X-RAY DIFFRACTION	19	chain 'C'
20	X-RAY DIFFRACTION	20	chain 'D'

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