PDB-8wm0: Crystal structure of TNIK-thiopeptide wTP3 complex

ID or keywords:

Entry

Database: PDB / ID: 8wm0

Title

Crystal structure of TNIK-thiopeptide wTP3 complex

Components

THIOPEPTIDE wTP3
TRAF2 and NCK-interacting protein kinase

Keywords

SIGNALING PROTEIN / RIPP / THIOPEPTIDE / KINASE INHIBITION / COMPLEX / SIGNALING PROTEIN-INHIBITOR COMPLEX

Function / homology

Function and homology information

microvillus assembly / regulation of dendrite morphogenesis / regulation of MAPK cascade / postsynaptic density, intracellular component / cytoskeleton organization / : / neuron projection morphogenesis / protein localization to plasma membrane / positive regulation of JNK cascade / recycling endosome ...
Similarity search - Function

Biological species

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Hamada, K. / Kobayashi, S. / Vinogradov, A.A. / Zhang, Y. / Goto, Y. / Suga, H. / Ogata, K. / Sengoku, T.

Funding support

1items

Citation

Journal: J.Am.Chem.Soc. / Year: 2024
Title: A Compact Reprogrammed Genetic Code for De Novo Discovery of Proteolytically Stable Thiopeptides.
Authors: Vinogradov, A.A. / Zhang, Y. / Hamada, K. / Kobayashi, S. / Ogata, K. / Sengoku, T. / Goto, Y. / Suga, H.

History

Deposition	Oct 1, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 27, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8wm0.cif.gz	138.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8wm0.ent.gz	103.2 KB	Display	PDB format
PDBx/mmJSON format	8wm0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8wm0_validation.pdf.gz	757 KB	Display	wwPDB validaton report
Full document	8wm0_full_validation.pdf.gz	760.8 KB	Display
Data in XML	8wm0_validation.xml.gz	13.8 KB	Display
Data in CIF	8wm0_validation.cif.gz	17.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wm/8wm0 ftp://data.pdbj.org/pub/pdb/validation_reports/wm/8wm0	HTTPS FTP

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Related structure data

Related structure data	7xzqS S: Starting model for refinement
Similar structure data	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	#265 - Jan 2022 Golgi Casein Kinase similarity (1)

Deposited unit

A: TRAF2 and NCK-interacting protein kinase

B: THIOPEPTIDE wTP3

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	53.720, 53.720, 220.170
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	TRAF2 and NCK-interacting protein kinase Mass: 35118.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TNIK, KIAA0551 / Production host: Escherichia coli (E. coli) References: UniProt: Q9UKE5, non-specific serine/threonine protein kinase
#2: Protein/peptide	THIOPEPTIDE wTP3 Mass: 1861.944 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.48 Å³/Da / Density % sol: 50.4 %
Crystal grow	Temperature: 283 K / Method: vapor diffusion, sitting drop / Details: 13% Tacsimate pH6.0

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 15, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.8→46.5 Å / Num. obs: 8896 / % possible obs: 100 % / Redundancy: 62.2 % / CC_1/2: 0.999 / Net I/σ(I): 25.2
Reflection shell	Resolution: 2.8→2.95 Å / Num. unique obs: 1291 / CC_1/2: 0.776

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7XZQ

7xzq

Resolution: 2.8→46.5 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.904 / SU B: 57.411 / SU ML: 0.487 / Cross valid method: NONE / ESU R Free: 0.462
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2852	880	9.962 %
R_work	0.227	7954	-
all	0.233	-	-
obs	-	8834	100 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 86.357 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.109 Å²	0.055 Å²	0 Å²
2-	-	0.109 Å²	-0 Å²
3-	-	-	-0.355 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→46.5 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2461	0	19	1	2481

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.013	2549
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.018	2314
X-RAY DIFFRACTION	r_angle_refined_deg	1.25	1.666	3477
X-RAY DIFFRACTION	r_angle_other_deg	1.04	1.599	5301
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.485	5	310
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.207	22.48	125
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	23.576	10	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.623	15	394
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.63	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.041	0.2	328
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	2921
X-RAY DIFFRACTION	r_gen_planes_other	0.004	0.02	590
X-RAY DIFFRACTION	r_nbd_refined	0.191	0.2	565
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.174	0.2	2313
X-RAY DIFFRACTION	r_nbtor_refined	0.157	0.2	1211
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	1300
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.111	0.2	55
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.153	0.2	19
X-RAY DIFFRACTION	r_nbd_other	0.189	0.2	47
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.079	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	0.595	4.972	1251
X-RAY DIFFRACTION	r_mcbond_other	0.585	4.968	1247
X-RAY DIFFRACTION	r_mcangle_it	1.029	7.455	1561
X-RAY DIFFRACTION	r_mcangle_other	1.019	7.452	1559
X-RAY DIFFRACTION	r_scbond_it	0.505	5.089	1298
X-RAY DIFFRACTION	r_scbond_other	0.504	5.091	1299
X-RAY DIFFRACTION	r_scangle_it	0.895	7.621	1915
X-RAY DIFFRACTION	r_scangle_other	0.895	7.623	1916
X-RAY DIFFRACTION	r_lrange_it	5.401	93.78	10194
X-RAY DIFFRACTION	r_lrange_other	5.4	93.775	10195

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 (%)
2.8-2.873	0.374	63	0.358	583	X-RAY DIFFRACTION	100
2.873-2.951	0.325	63	0.346	572	X-RAY DIFFRACTION	100
2.951-3.036	0.419	63	0.32	545	X-RAY DIFFRACTION	100
3.036-3.129	0.356	60	0.315	549	X-RAY DIFFRACTION	100
3.129-3.231	0.365	55	0.296	533	X-RAY DIFFRACTION	100
3.231-3.344	0.304	61	0.277	505	X-RAY DIFFRACTION	100
3.344-3.47	0.336	48	0.269	469	X-RAY DIFFRACTION	100
3.47-3.611	0.368	51	0.236	490	X-RAY DIFFRACTION	100
3.611-3.77	0.271	54	0.258	428	X-RAY DIFFRACTION	100
3.77-3.953	0.292	47	0.234	439	X-RAY DIFFRACTION	100
3.953-4.165	0.254	47	0.213	416	X-RAY DIFFRACTION	100
4.165-4.415	0.221	45	0.177	389	X-RAY DIFFRACTION	100
4.415-4.717	0.271	36	0.172	363	X-RAY DIFFRACTION	100
4.717-5.091	0.23	38	0.195	338	X-RAY DIFFRACTION	100
5.091-5.57	0.294	36	0.203	313	X-RAY DIFFRACTION	100
5.57-6.216	0.324	31	0.249	285	X-RAY DIFFRACTION	100
6.216-7.157	0.23	26	0.213	259	X-RAY DIFFRACTION	100
7.157-8.714	0.246	28	0.179	211	X-RAY DIFFRACTION	100
8.714-12.112	0.234	17	0.156	163	X-RAY DIFFRACTION	100
12.112-46.5	0.309	11	0.273	105	X-RAY DIFFRACTION	100

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	5.0828	-0.6956	-0.7961	3.0265	-0.3993	8.6918	-0.2959	0.4352	0.0397	-0.2313	0.0001	0.0325	1.1145	-0.4341	0.2957	0.2987	0.046	0.0845	0.3903	-0.2346	0.4502	-5.874	-2.208	29.1327
2	6.6252	0.1722	3.9688	2.3518	0.5167	2.4766	-0.0399	0.0534	0.2293	-0.0466	-0.1235	-0.3002	0.0304	-0.0454	0.1634	0.1517	-0.105	0.1839	0.6263	-0.3641	0.3809	-12.6666	1.9746	24.8385
3	5.7088	1.3353	0.6435	5.2022	2.1586	4.5205	-0.3825	-0.5003	0.9424	-0.4503	-0.4995	0.7765	-0.6146	-0.8408	0.882	0.1225	0.0881	-0.1026	0.2881	-0.3684	0.5074	-26.9435	8.2778	13.3388
4	3.9521	1.5463	-0.2727	3.5761	-5.8334	11.1993	-0.1862	-0.7659	-0.2972	-0.161	-0.3047	-0.475	0.2555	0.2143	0.4909	0.3343	0.0014	0.0302	0.3527	-0.223	0.4588	-9.7872	-0.626	4.5575

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	12 - 63
2	X-RAY DIFFRACTION	2	ALL	A	64 - 126
3	X-RAY DIFFRACTION	3	ALL	A	127 - 310
4	X-RAY DIFFRACTION	4	ALL	B	2 - 14

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