PDB-7vkr: Crystal structure of D. melanogaster SAMTOR in complex with SAM

ID or keywords:

Entry

Database: PDB / ID: 7vkr

Title

Crystal structure of D. melanogaster SAMTOR in complex with SAM

Components

S-adenosylmethionine sensor upstream of mTORC1

Keywords

TRANSFERASE / SAMTOR / SAM

Function / homology

Function and homology information

amino acid sensor activity / cellular response to methionine / S-adenosyl-L-methionine binding / negative regulation of TORC1 signaling / cellular response to amino acid starvation / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation / protein-containing complex binding
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.1 Å

Authors

Tang, X. / Zhang, T. / Ding, J.

Funding support

China, 1items

Citation

Journal: Sci Adv / Year: 2022
Title: Molecular mechanism of S -adenosylmethionine sensing by SAMTOR in mTORC1 signaling.
Authors: Tang, X. / Zhang, Y. / Wang, G. / Zhang, C. / Wang, F. / Shi, J. / Zhang, T. / Ding, J.

History

Deposition	Sep 30, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 20, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7vkr.cif.gz	377.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7vkr.ent.gz	306.5 KB	Display	PDB format
PDBx/mmJSON format	7vkr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7vkr_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	7vkr_full_validation.pdf.gz	1.3 MB	Display
Data in XML	7vkr_validation.xml.gz	36 KB	Display
Data in CIF	7vkr_validation.cif.gz	51.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vk/7vkr ftp://data.pdbj.org/pub/pdb/validation_reports/vk/7vkr	HTTPS FTP

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Related structure data

Related structure data	7vkkC 7vkqC C: citing same article (ref.)
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	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: S-adenosylmethionine sensor upstream of mTORC1

B: S-adenosylmethionine sensor upstream of mTORC1

C: S-adenosylmethionine sensor upstream of mTORC1

D: S-adenosylmethionine sensor upstream of mTORC1

hetero molecules

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

1

A: S-adenosylmethionine sensor upstream of mTORC1

hetero molecules

defined by author&software
Evidence: light scattering
35.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: S-adenosylmethionine sensor upstream of mTORC1

hetero molecules

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

3

C: S-adenosylmethionine sensor upstream of mTORC1

hetero molecules

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

4

D: S-adenosylmethionine sensor upstream of mTORC1

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.269, 64.095, 79.274
Angle α, β, γ (deg.)	90.100, 93.270, 96.610
Int Tables number	1
Space group name H-M	P1

#1: Protein	S-adenosylmethionine sensor upstream of mTORC1 / dSamtor / Probable methyltransferase BMT2 homolog Mass: 35340.430 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Samtor, CG3570 / Production host: Escherichia coli (E. coli) References: UniProt: Q9W138, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 427 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 1.79 Å³/Da / Density % sol: 31.36 %
Crystal grow	Temperature: 289 K / Method: evaporation Details: 0.1 M sodium citrate, pH 5.0, and 20% (w/v) PEG 8,000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 4, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 2.1→43.322 Å / Num. obs: 51008 / % possible obs: 88.5 % / Redundancy: 4.2 % / CC_1/2: 0.995 / R_merge(I) obs: 0.127 / Net I/σ(I): 9.5
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.841 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3585 / CC_1/2: 0.602 / % possible all: 59.6

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Processing

Software

Name	Version	Classification
PHENIX	1.12_2829	refinement
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.1→43.322 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2387	2018	3.96 %
R_work	0.1875	48879	-
obs	0.1896	50897	88.85 %

Solvent computation

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

Displacement parameters

B_iso max: 98.05 Å² / B_iso mean: 29.5429 Å² / B_iso min: 6.66 Å²

Refinement step

Cycle: final / Resolution: 2.1→43.322 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6897	0	147	427	7471
B_iso mean	-	-	26.1	31.09	-
Num. residues	-	-	-	-	855

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	7196
X-RAY DIFFRACTION	f_angle_d	1.007	9745
X-RAY DIFFRACTION	f_chiral_restr	0.055	1081
X-RAY DIFFRACTION	f_plane_restr	0.006	1239
X-RAY DIFFRACTION	f_dihedral_angle_d	18.616	4399

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
2.1-2.1525	0.2805	106	0.2472	2428	62
2.1525-2.2107	0.3312	102	0.2423	2622	66
2.2107-2.2758	0.2917	123	0.2329	2870	73
2.2758-2.3492	0.2781	124	0.2245	3109	80
2.3492-2.4332	0.264	131	0.2142	3340	85
2.4332-2.5306	0.2589	160	0.2188	3642	93
2.5306-2.6457	0.2594	166	0.2113	3857	97
2.6457-2.7852	0.2245	159	0.2031	3789	97
2.7852-2.9597	0.2841	145	0.1845	3870	98
2.9597-3.1881	0.2461	162	0.1828	3861	98
3.1881-3.5088	0.2252	153	0.1692	3852	98
3.5088-4.0162	0.1903	162	0.1519	3861	99
4.0162-5.0588	0.1918	161	0.1502	3906	99
5.0588-43.322	0.2427	164	0.2006	3872	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	2.4264	0.6498	1.2443	7.8869	1.0571	1.8058	0.1294	0.7523	-0.2995	-0.6521	-0.066	-0.6855	0.4034	0.3103	-0.0296	0.2195	0.0789	0.039	0.201	-0.0444	0.1562	38.8663	39.829	81.0934
2	3.2506	-1.687	2.2263	8.4091	-8.7665	9.24	-0.2409	-0.2089	-0.4956	0.1206	0.0219	-0.141	0.6897	0.5228	0.1938	0.3291	0.0678	0.0482	0.1675	-0.0215	0.267	37.8612	24.2349	96.4837
3	3.8655	-2.0985	1.8855	8.8903	-6.5724	5.0844	-0.2482	-0.026	-0.4946	-0.459	0.2979	0.6837	0.5537	-0.3477	-0.2862	0.4062	-0.1313	0.0355	0.2773	0.003	0.3925	28.0805	29.6095	93.983
4	3.7581	0.1227	-0.9407	4.5164	1.6442	3.1958	0.2052	0.4468	0.1685	-0.8177	-0.3071	0.1209	-0.1783	-0.295	0.0599	0.2421	0.034	-0.0262	0.1457	0.0141	0.0949	29.2948	53.0212	84.0457
5	6.3988	0.3321	0.3635	5.1666	-2.0496	6.5951	0.1155	0.33	0.4198	0.0858	-0.0469	0.8276	-0.2912	-0.412	0.0136	0.1232	0.0093	-0.0205	0.1551	-0.0304	0.1743	19.8897	52.5533	95.0668
6	3.2433	0.0305	-0.719	2.9369	-0.1046	3.3854	0.0669	-0.1893	0.2218	-0.0453	-0.0069	-0.2106	-0.3043	0.3097	-0.0428	0.0791	-0.0223	-0.0143	0.1222	-0.0345	0.1155	34.7356	47.3903	95.4249
7	5.3414	-1.2724	0.9884	9.1141	-0.1268	8.2976	0.0021	-0.3412	0.7065	0.3897	0.2668	-1.3731	-0.7409	1.5168	-0.1737	0.2411	-0.0067	-0.1178	0.3901	-0.0372	0.3429	44.5979	41.9244	102.4235
8	1.1908	0.6427	-1.3345	5.3081	-2.8372	2.7947	0.0195	-0.2257	0.0467	-0.0754	-0.3696	-0.5978	-0.0321	0.4205	0.3324	0.1602	0.0323	-0.0046	0.1271	-0.0095	0.2138	44.0538	41.6132	91.0749
9	9.2757	2.4887	1.4128	6.6193	2.3407	4.6905	0.0674	-0.9187	-0.8692	0.9203	0.1455	-0.1835	0.4427	0.098	-0.2039	0.2699	0.0723	0.004	0.1974	0.085	0.2115	37.3176	31.6504	104.6237
10	1.0627	-0.254	1.2362	9.0614	0.7691	4.9363	0.1219	-1.1445	0.379	1.4644	0.0071	-1.8747	-0.1299	0.8638	-0.0824	0.5715	-0.0179	-0.1748	0.9792	-0.1579	0.7352	46.5027	44.0764	107.4314
11	1.3094	0.1852	-0.0461	2.7743	0.4902	0.2628	0.3996	0.7481	0.3273	-0.9164	-0.3037	0.416	-0.1626	-0.0368	-0.0702	0.532	0.1135	-0.0638	0.1875	0.079	0.0193	38.3665	19.4589	41.4436
12	2.4546	-2.2728	-3.5743	3.3915	6.1382	2.0293	-0.2862	-0.1487	0.4982	-0.0351	0.0358	0.1226	-1.0917	-0.5915	0.125	0.5656	-0.0106	-0.0265	0.1487	0.0113	0.2552	37.5775	34.1619	56.3058
13	2.5627	-0.9755	-1.1666	3.8132	1.8411	4.8396	0.2019	-0.0301	0.5931	-0.571	0.1237	-0.7804	-1.1215	0.4432	-0.3321	0.3821	-0.0795	0.0074	0.264	0.0228	0.2914	46.4809	25.8862	54.6012
14	3.0906	-0.1523	0.7739	4.2182	-1.7526	3.6666	0.0549	0.5663	-0.0337	-1.0628	-0.2384	-0.1283	-0.1158	0.0852	0.102	0.4433	0.0877	0.0325	0.2534	-0.022	0.1306	46.4162	8.9592	42.0265
15	5.339	1.1641	2.4188	4.6648	4.3444	7.2607	0.1935	0.3352	-0.2882	-0.3031	0.149	-0.6528	0.2672	0.5958	-0.2772	0.232	0.0531	0.0378	0.1667	0.0282	0.1542	52.9767	3.59	54.1351
16	3.3911	-0.5853	0.6106	3.5219	-0.0306	4.2107	0.1433	-0.0193	-0.1787	-0.2315	-0.1155	0.1747	0.2597	-0.2621	-0.0227	0.186	-0.0108	0.0028	0.1247	0.0142	0.0715	40.4868	11.3281	55.9273
17	2.0726	0.3357	1.5762	9.1883	2.3935	2.0392	0.2585	-0.4743	-0.0705	0.1454	-0.108	1.0118	0.7236	-1.1546	-0.1643	0.2253	-0.0449	0.037	0.3872	0.0442	0.2573	29.7943	16.5248	61.8337
18	3.5559	0.58	1.5981	5.0788	2.6708	2.5638	0.1898	-0.4367	-0.0591	0.3665	-0.2765	0.4878	0.212	-0.5961	0.0767	0.2555	-0.0043	0.0008	0.2239	0.0318	0.1641	31.9944	18.8266	58.9498
19	1.0438	0.3256	-0.5603	7.7461	-4.8264	4.4648	-0.1056	0.069	-0.0653	0.5179	0.2148	0.7776	-0.0142	-0.2215	-0.1264	0.1262	-0.0083	0.0314	0.1473	-0.0318	0.1777	41.5077	14.4373	79.1979
20	4.471	3.7561	3.3877	5.1566	4.0433	4.0585	0.0166	0.0878	0.1991	0.0053	0.4942	-0.7613	-0.2296	0.5639	-0.3564	0.1868	-0.0449	-0.0581	0.2051	-0.0415	0.3588	55.4863	29.8962	79.9569
21	4.2655	-0.3975	0.1823	2.4813	-0.1538	2.5633	-0.0485	0.1397	-0.3219	-0.1901	0.0455	-0.3872	0.2649	0.2761	0.0119	0.1356	0.0322	0.0543	0.1386	-0.0078	0.1773	54.7003	2.7051	75.1651
22	3.9979	-0.5491	-0.2294	3.2691	0.6653	4.1766	-0.1842	-0.371	-0.284	0.6371	0.1129	-0.7776	0.4836	0.3947	0.087	0.2115	0.0571	-0.0729	0.2126	0.0183	0.3149	60.2759	5.9785	81.7416
23	0.5911	-0.7754	-0.0138	2.4473	0.9999	1.2928	-0.4728	-0.6365	0.0336	1.6173	0.4468	-0.1763	0.1155	0.1772	0.0293	0.2476	0.0245	-0.1225	0.2632	-0.0326	0.1632	51.2231	16.0559	88.4271
24	2.3615	0.5678	-0.1817	6.2404	0.451	1.3839	-0.3651	-0.4938	0.6538	0.631	0.236	-0.3483	-0.0889	0.242	0.0691	0.2849	0.094	-0.1453	0.3141	-0.0924	0.2308	61.274	26.839	91.305
25	2.0765	-1.7317	-0.2875	8.4756	3.4926	7.3081	-0.0694	-0.1879	-0.0237	0.6599	0.3346	-0.8591	-0.1913	0.6133	-0.2228	0.2069	0.0104	-0.054	0.1863	0.0236	0.1526	36.2317	45.4623	39.4961
26	5.9857	4.3317	-3.0654	5.01	-3.0029	4.3961	0.2272	-0.0609	-0.777	-0.1668	0.3588	1.1408	0.8778	-0.3769	-0.3316	0.3078	-0.0632	0.0471	0.2638	0.1323	0.6054	22.0901	29.4113	38.2854
27	4.64	-0.8467	-0.2971	3.8894	0.6974	2.9242	-0.0808	0.1049	0.2658	0.18	0.0377	0.401	-0.3728	-0.3437	0.0487	0.1971	0.06	0.012	0.1923	0.0208	0.1234	23.1418	56.4629	33.9791
28	3.333	0.0384	-0.099	2.3858	-0.7121	2.9858	-0.1895	-0.593	0.1198	0.5926	0.2094	0.847	-0.8225	-0.6299	0.04	0.3397	0.1513	0.1015	0.3479	0.0126	0.3559	17.0466	52.8529	40.1094
29	0.9589	-0.611	-1.3006	1.8223	-0.3412	3.094	-0.3294	-0.7064	-0.3734	1.6643	0.4895	0.4372	0.0965	-0.1867	-0.0513	0.4789	0.1393	0.1119	0.405	0.1496	0.2233	24.0298	42.6334	47.8148
30	2.0638	0.3191	0.6459	2.4059	-0.5155	0.3055	-0.2603	-1.0455	-0.4244	1.231	0.3833	0.551	-0.2764	-0.5885	-0.1186	0.4549	0.083	0.2662	0.4825	0.2941	0.4137	21.236	38.1773	48.0278

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 71 through 89 )	A	71 - 89
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 90 through 108 )	A	90 - 108
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 109 through 125 )	A	109 - 125
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 126 through 162 )	A	126 - 162
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 163 through 186 )	A	163 - 186
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 187 through 239 )	A	187 - 239
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 240 through 252 )	A	240 - 252
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 253 through 272 )	A	253 - 272
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 273 through 285 )	A	273 - 285
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 286 through 298 )	A	273 - 298
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 72 through 89 )	B	72 - 89
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 90 through 107 )	B	90 - 107
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 108 through 131 )	B	108 - 131
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 132 through 149 )	B	132 - 149
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 150 through 186 )	B	150 - 186
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 187 through 239 )	B	187 - 239
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 240 through 252 )	B	240 - 252
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 253 through 298 )	B	253 - 298
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 71 through 89 )	C	71 - 89
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 90 through 125 )	C	90 - 125
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 126 through 175 )	C	126 - 175
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 176 through 218 )	C	176 - 218
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 219 through 275 )	C	219 - 275
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 276 through 286 )	C	276 - 286
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 68 through 89 )	D	68 - 89
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 90 through 125 )	D	90 - 125
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 126 through 175 )	D	126 - 175
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 176 through 218 )	D	176 - 218
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 219 through 262 )	D	219 - 262
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 263 through 287 )	D	263 - 287

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Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi