PDB-7a0m: TSC1 N-terminal domain

ID or keywords:

Entry

Database: PDB / ID: 7a0m

Title

TSC1 N-terminal domain

Components

TSC1 N-terminal domain

Keywords

SIGNALING PROTEIN / TSC / GAP / GTPase signaling

Function / homology

Hamartin / Hamartin protein / TSC1-TSC2 complex / negative regulation of TOR signaling / Armadillo-type fold / regulation of cell cycle / Uncharacterized protein

Function and homology information

Biological species

Chaetomium thermophilum (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.32 Å

Authors

Zech, R. / Kiontke, S. / Kuemmel, D.

Funding support

Germany, 1items

Citation

Journal: Mol.Cell / Year: 2021
Title: TSC1 binding to lysosomal PIPs is required for TSC complex translocation and mTORC1 regulation.
Authors: Fitzian, K. / Bruckner, A. / Brohee, L. / Zech, R. / Antoni, C. / Kiontke, S. / Gasper, R. / Linard Matos, A.L. / Beel, S. / Wilhelm, S. / Gerke, V. / Ungermann, C. / Nellist, M. / Raunser, ...

History

Deposition	Aug 10, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 26, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jul 14, 2021	Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2	Oct 9, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7a0m.cif.gz	601.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7a0m.ent.gz	503.3 KB	Display	PDB format
PDBx/mmJSON format	7a0m.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/a0/7a0m ftp://data.pdbj.org/pub/pdb/validation_reports/a0/7a0m	HTTPS FTP

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Related structure data

Related structure data	7a0nC C: citing same article (ref.)
Similar structure data	7a0m-2 6fj3-d 3duz-d 3si7-d 6fla-d 2ddb-d 4r9y-d 7m7w-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: TSC1 N-terminal domain

B: TSC1 N-terminal domain

C: TSC1 N-terminal domain

D: TSC1 N-terminal domain

hetero molecules

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

1

A: TSC1 N-terminal domain

B: TSC1 N-terminal domain

hetero molecules

defined by author&software
Evidence: light scattering
96.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: TSC1 N-terminal domain

D: TSC1 N-terminal domain

defined by author&software
Evidence: light scattering
96.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	141.085, 150.744, 111.880
Angle α, β, γ (deg.)	90.00, 108.47, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	TSC1 N-terminal domain Mass: 48245.148 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0033260 / Production host: Escherichia coli (E. coli) / References: UniProt: G0S5K3
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.93 Å³/Da / Density % sol: 58.06 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, hanging drop Details: 0.1 M bicine trizma (pH 8.5), 16% (w/v) PEG 3350, 12.5% (w/v) PEG 1000, 12.5 % (v/v) MPD, 0.03 M sodium nitrate, 0.03 M sodium phosphate dibasic and 0.03 M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.977 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 17, 2016
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.977 Å / Relative weight: 1
Reflection	Resolution: 2.32→44.9 Å / Num. obs: 95121 / % possible obs: 98.9 % / Redundancy: 3.4 % / CC_1/2: 0.998 / R_rim(I) all: 0.064 / Net I/σ(I): 13.2
Reflection shell	Resolution: 2.32→2.4 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 15143 / CC_1/2: 0.764 / R_rim(I) all: 0.696

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Processing

Software

Name	Version	Classification
PHENIX	(1.12rc1_2807: ???)	refinement
XDS		data reduction
XSCALE		data scaling
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.32→44.9 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2699	2098	2.21 %
R_work	0.2401	-	-
obs	0.2408	94957	99.17 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.32→44.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11818	0	5	34	11857

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	12149
X-RAY DIFFRACTION	f_angle_d	0.596	16532
X-RAY DIFFRACTION	f_dihedral_angle_d	10.568	7240
X-RAY DIFFRACTION	f_chiral_restr	0.04	1814
X-RAY DIFFRACTION	f_plane_restr	0.005	2120

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 (%)
2.32-2.374	0.3443	139	0.3282	6150	X-RAY DIFFRACTION	99
2.374-2.4334	0.3196	140	0.3116	6190	X-RAY DIFFRACTION	99
2.4334-2.4992	0.3264	140	0.299	6201	X-RAY DIFFRACTION	99
2.4992-2.5727	0.3725	139	0.2909	6169	X-RAY DIFFRACTION	99
2.5727-2.6557	0.3368	140	0.2802	6191	X-RAY DIFFRACTION	99
2.6557-2.7506	0.2907	140	0.2836	6183	X-RAY DIFFRACTION	100
2.7506-2.8607	0.3231	140	0.279	6197	X-RAY DIFFRACTION	99
2.8607-2.9909	0.3344	139	0.2758	6180	X-RAY DIFFRACTION	99
2.9909-3.1486	0.3037	140	0.2767	6177	X-RAY DIFFRACTION	99
3.1486-3.3458	0.2827	140	0.2695	6189	X-RAY DIFFRACTION	99
3.3458-3.604	0.312	140	0.2512	6222	X-RAY DIFFRACTION	99
3.604-3.9665	0.2655	140	0.2318	6211	X-RAY DIFFRACTION	99
3.9665-4.54	0.2123	139	0.2012	6166	X-RAY DIFFRACTION	99
4.54-5.718	0.2247	141	0.2086	6230	X-RAY DIFFRACTION	99
5.718-44.9	0.2414	141	0.2159	6203	X-RAY DIFFRACTION	98

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	3.4728	1.2173	1.469	3.0044	2.0762	5.5306	0.3845	-0.037	-0.3621	0.4149	-0.0197	-0.422	0.6448	0.4489	-0.2525	0.5769	0.1284	-0.1136	0.5221	-0.0001	0.3883	29.728	-101.7183	87.6842
2	0.9834	-0.461	-0.2184	2.0563	0.9278	4.1146	-0.0978	-0.1454	0.0338	0.1956	0.0783	0.1029	0.1394	-0.4644	-0.0022	0.3272	-0.007	-0.0242	0.4095	-0.0348	0.2954	16.5982	-113.2756	50.0484
3	5.6103	-0.9598	2.3225	4.8242	-1.0646	6.9274	-0.1943	0.989	1.2419	-1.9002	-0.0916	0.3955	-1.1043	-0.6355	0.2741	1.1633	0.1381	-0.0898	1.7069	0.2611	0.5906	14.0533	-91.9451	-38.2227
4	0.4181	-1.0294	0.5583	2.6711	-0.6382	3.2735	0.5567	0.5738	-0.1406	-0.8935	-0.8904	0.5518	0.323	-0.458	-0.2443	1.1485	0.0302	-0.2012	1.4254	-0.041	0.5499	18.1994	-104.5052	-38.4158
5	2.7827	0.6944	2.1631	4.3549	-1.36	5.7353	0.0694	0.9376	0.4647	-0.1929	-0.2148	-0.5223	-0.6761	-0.8938	0.1051	0.888	0.0443	-0.0843	1.0497	0.2913	0.894	23.1938	-96.1189	-31.3228
6	4.7205	-1.2515	2.6268	4.7199	0.9784	2.541	0.602	1.3858	0.019	-1.0032	-0.548	-0.7268	1.3005	-0.055	0.3179	0.7619	-0.1883	-0.0624	0.6984	0.1764	0.5776	27.4066	-103.3074	-26.3951
7	3.0644	-4.0395	2.375	6.2738	-1.798	7.3687	-0.2911	-0.361	1.5042	0.7937	-0.475	-1.248	-0.814	-0.2256	0.4884	0.7359	0.0692	-0.1598	0.7896	0.1125	0.7976	24.4148	-94.4362	-20.3664
8	0.1162	-0.2076	0.7741	1.2465	-1.4011	6.183	-0.1398	0.5209	0.1662	-0.4383	0.0244	-0.023	0.0837	0.0263	0.2236	0.4354	-0.134	0.0232	0.6166	0.0251	0.3714	29.8749	-111.654	-2.1323
9	2.6594	-0.1057	-1.2067	1.8707	-0.5502	3.782	-0.0957	0.3468	0.0848	0.0479	0.044	-0.223	0.0835	0.0094	0.0578	0.3434	-0.0679	-0.0268	0.3811	-0.0643	0.3147	30.1041	-116.425	19.0628
10	6.5548	-1.6313	1.6315	4.716	-1.5998	3.5261	0.3451	0.0216	-1.4249	-0.0666	0.0161	0.6782	0.1861	-0.7767	-0.0456	0.5068	0.081	0.1627	0.7774	0.076	0.9253	-23.5186	-176.9274	72.2615
11	8.0221	-3.6533	2.7181	3.434	-2.6195	2.4325	-0.1666	-0.5479	0.7387	0.4313	0.1366	0.4258	-0.7366	-0.188	-0.0229	0.6644	0.092	0.1429	1.0313	-0.0199	0.9289	-21.1845	-165.8204	78.3867
12	2.376	-1.4439	-0.2829	5.0888	0.169	5.1135	-0.1597	-0.7984	0.4497	0.4524	0.1548	-0.5683	0.1018	-0.2419	0.0074	0.4621	0.0295	0.0674	0.6735	0.1147	0.6843	-12.2939	-171.7699	73.221
13	2.5677	-0.6593	-1.5819	0.5931	-0.0598	2.3734	0.105	0.0353	0.7717	-0.0092	-0.2385	-0.0035	-0.5059	-0.0306	-0.0364	0.5439	0.0599	0.0419	0.4632	0.048	0.7987	-5.7978	-167.3771	69.5205
14	1.1585	1.5744	-1.3608	2.4636	-1.0461	4.399	0.0214	-0.2719	0.3799	0.5086	0.1517	0.0539	-0.8025	-0.1676	-0.3574	0.6853	-0.0055	0.1223	0.7225	0.1443	0.6452	1.761	-160.3453	64.114
15	2.135	0.6056	-2.0373	2.7297	-1.9146	3.8831	0.2071	-0.537	0.0466	0.486	0.0822	0.199	-0.3759	-0.001	-0.2804	0.5396	-0.0598	0.0226	0.4201	-0.0075	0.3961	13.3362	-149.8128	52.6275
16	2.0101	0.1402	-0.1864	1.9549	-0.937	3.8302	0.0421	-0.3989	0.0528	0.0194	0.0267	-0.0301	0.1826	-0.0213	-0.0708	0.3925	-0.0101	0.0058	0.3391	-0.0449	0.3632	22.4342	-148.0499	38.8751
17	0.1469	0.0939	0.192	0.1342	0.1191	0.2574	0.5957	-0.2909	-0.7429	-0.0813	-0.273	-0.902	0.0866	0.8252	0.2169	1.0682	-0.1834	0.53	1.5598	-0.1287	1.8554	74.5506	-170.5761	-19.2364
18	0.8815	0.249	-0.7857	0.2227	-0.5334	1.3662	0.0764	0.4962	1.0935	-0.1693	-0.0508	-0.274	-1.1114	0.7664	0.1019	0.9988	-0.1472	0.3267	1.1195	-0.0268	1.4337	74.7579	-158.1278	-18.7825
19	4.5909	-3.5634	-2.191	3.526	2.5179	4.0373	0.2886	0.2095	0.1352	-0.8667	-0.193	-0.8766	-0.2107	0.2329	0.0361	0.7238	-0.0296	0.2386	0.6259	-0.0956	0.7511	60.5801	-163.2629	-16.1893
20	5.4926	-3.919	-2.7501	4.2428	-0.1787	4.8004	-0.0436	0.5168	-0.2138	-0.7421	-0.2466	-0.1922	-0.0719	-0.6458	-0.03	0.6375	-0.0429	0.2419	0.624	-0.2069	0.6274	49.775	-157.5907	-9.7329
21	1.879	0.0813	-0.8676	1.8006	1.184	4.5951	0.0478	0.5209	-0.1754	-0.3535	0.1282	-0.0702	-0.028	-0.1397	-0.1849	0.5356	-0.0365	0.0327	0.3661	-0.0889	0.4349	29.088	-150.1948	6.9522

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 165 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 166 through 413 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 6 through 39 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 40 through 62 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 63 through 86 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 87 through 104 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 105 through 123 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 124 through 277 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 278 through 413 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 3 through 39 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 40 through 62 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 63 through 86 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 87 through 123 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 124 through 181 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 182 through 277 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 278 through 412 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 9 through 28 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 29 through 62 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 63 through 123 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 124 through 181 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 182 through 413 )

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