PDB-7vkq: Crystal structure of D. melanogaster SAMTOR in the SAH bound form

ID or keywords:

Entry

Database: PDB / ID: 7vkq

Title

Crystal structure of D. melanogaster SAMTOR in the SAH bound form

Components

S-adenosylmethionine sensor upstream of mTORC1

Keywords

TRANSFERASE / SAMTOR / SAH

Function / homology

Function and homology information

S-adenosyl-L-methionine binding / negative regulation of TORC1 signaling / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation
Similarity search - Function

Biological species

Drosophila melanogaster (fruit fly)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.094 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 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7vkq.cif.gz	383.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7vkq.ent.gz	311.8 KB	Display	PDB format
PDBx/mmJSON format	7vkq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7vkq_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	7vkq_full_validation.pdf.gz	1.5 MB	Display
Data in XML	7vkq_validation.xml.gz	40.2 KB	Display
Data in CIF	7vkq_validation.cif.gz	57 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vk/7vkq ftp://data.pdbj.org/pub/pdb/validation_reports/vk/7vkq	HTTPS FTP

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Related structure data

Related structure data	7vkkSC 7vkrC S: Starting model for refinement 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

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

142 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
Evidence: light scattering
35.4 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
35.4 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
35.4 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
35.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	49.934, 63.992, 80.268
Angle α, β, γ (deg.)	90.260, 93.380, 96.790
Int Tables number	1
Space group name H-M	P1

#1: Protein	S-adenosylmethionine sensor upstream of mTORC1 / dSamtor / Probable methyltransferase BMT2 homolog Mass: 35012.164 Da / Num. of mol.: 4 / Fragment: trasnferase 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-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 598 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 1.82 Å³/Da / Density % sol: 32.24 %
Crystal grow	Temperature: 290 K / Method: evaporation / pH: 5 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: BL18U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.09→49.49 Å / Num. obs: 54989 / % possible obs: 94.8 % / Redundancy: 2 % / CC_1/2: 0.993 / R_merge(I) obs: 0.105 / Net I/σ(I): 6.1
Reflection shell	Resolution: 2.09→2.14 Å / R_merge(I) obs: 0.54 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4909 / CC_1/2: 0.678 / % possible all: 78.5

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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:

MOLECULAR REPLACEMENT
Starting model: 7VKK

7vkk

Resolution: 2.094→41.022 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2062	1995	3.63 %
R_work	0.1662	52981	-
obs	0.1676	54976	94.82 %

Solvent computation

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

Displacement parameters

B_iso max: 75.94 Å² / B_iso mean: 26.4826 Å² / B_iso min: 6.14 Å²

Refinement step

Cycle: final / Resolution: 2.094→41.022 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7025	0	104	598	7727
B_iso mean	-	-	16.33	32.13	-
Num. residues	-	-	-	-	873

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7344
X-RAY DIFFRACTION	f_angle_d	0.94	9957
X-RAY DIFFRACTION	f_chiral_restr	0.054	1109
X-RAY DIFFRACTION	f_plane_restr	0.006	1268
X-RAY DIFFRACTION	f_dihedral_angle_d	18.134	4495

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 (%)
2.094-2.1463	0.307	117	0.2526	3192	80
2.1463-2.2043	0.2812	133	0.2168	3582	90
2.2043-2.2692	0.2325	135	0.2079	3717	93
2.2692-2.3424	0.2853	144	0.2015	3771	95
2.3424-2.4261	0.2832	155	0.1959	3811	95
2.4261-2.5233	0.2316	134	0.1989	3820	95
2.5233-2.6381	0.2308	147	0.1815	3904	97
2.6381-2.7771	0.2093	141	0.1681	3906	97
2.7771-2.9511	0.2306	156	0.1655	3865	98
2.9511-3.1789	0.1899	140	0.1597	3872	97
3.1789-3.4986	0.1916	154	0.1497	3887	98
3.4986-4.0045	0.1442	143	0.1285	3941	98
4.0045-5.0438	0.1599	152	0.1253	3856	97
5.0438-41.022	0.184	144	0.1713	3857	97

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	3.8534	1.6312	2.4994	7.8681	1.007	1.6366	-0.4582	0.7459	-0.2163	-0.9721	0.0007	-0.4054	0.0734	0.2831	0.2734	0.2455	0.0234	0.1154	0.1245	-0.1168	0.2025	39.841	20.099	40.091
2	2.0086	-0.8769	0.939	5.3833	-6.6458	2.0262	-0.2825	-0.2106	-0.8173	0.3046	-0.312	-0.6116	0.5381	0.8433	0.5209	0.4876	0.1234	-0.0255	0.1441	-0.0039	0.6217	38.578	36.524	57.381
3	3.6429	-1.1593	1.7154	6.2948	-2.8628	4.8107	0.0515	-0.1272	-0.996	-0.3125	0.3291	0.5405	0.5858	-0.2061	-0.4025	0.1778	0.0117	0.0245	0.1993	-0.02	0.3525	48.836	27.374	53.871
4	3.8861	-0.1871	-0.4147	4.7728	3.197	6.4909	-0.0311	0.3958	-0.0068	-0.6173	-0.1225	0.2304	-0.1442	-0.1306	0.1355	0.1776	0.0128	-0.0228	0.1233	0.0072	0.0791	49.271	7.105	44.485
5	6.7202	-0.4205	-0.328	5.8237	-2.801	4.9075	-0.0245	0.1222	0.5599	0.042	0.2311	0.8264	-0.1359	-0.4317	-0.1616	0.101	0.0064	0.0302	0.1642	-0.0201	0.1993	56.81	8.503	57.543
6	3.5974	-1.2533	-1.1177	2.9631	0.0727	4.6	0.0116	-0.0871	0.157	0.0476	-0.0778	-0.2309	-0.4398	0.1488	-0.0325	0.1264	0.0168	-0.0159	0.0555	-0.0183	0.0883	43.505	11.4	53.446
7	6.0395	0.2409	0.1947	3.8619	0.5597	4.3639	0.1627	-0.4934	0.3838	0.3992	-0.1297	-0.1376	-0.2467	0.2501	-0.0028	0.1492	-0.024	-0.004	0.135	-0.0069	0.0816	43.142	12.557	61.747
8	2.5627	-1.1957	-0.77	3.2978	0.0511	4.0527	0.0457	-0.1072	-0.2434	0.161	-0.0429	-0.4757	-0.0472	0.3704	0.0115	0.0899	0.0104	-0.0145	0.1	-0.0099	0.1114	39.51	17.57	51.862
9	6.1182	4.7964	-2.6816	6.5804	2.2784	2.038	0.1752	-0.6954	0.1165	0.1661	0.2149	-0.7454	-0.1723	1.0863	-0.3993	0.2304	-0.0127	-0.0493	0.3689	0.0315	0.3077	31.586	18.456	61.386
10	1.6814	0.4146	-0.6959	5.0106	-1.5506	1.6578	-0.0752	0.044	-0.3284	-0.1619	-0.114	-0.6644	0.1824	0.2004	0.2235	0.141	0.0412	0.0027	0.1166	-0.0195	0.2494	34.686	20.634	51.3
11	6.9363	0.9818	0.989	8.8546	0.7371	5.752	0.2928	-0.7956	-0.0549	1.0528	-0.1322	-1.1494	-0.1585	0.9928	-0.0855	0.2592	-0.0244	-0.0384	0.3949	0.0945	0.3495	31.98	19.69	65.843
12	4.3315	0.6454	-0.9701	4.6061	-1.4417	1.9595	-0.1975	0.9558	-0.706	-1.0825	-0.2984	0.484	-0.2979	-0.3422	0.2023	0.4897	0.0894	0.0282	0.1069	0.2645	-0.2539	40.226	43.263	80.209
13	2.6776	-2.8875	-4.8037	3.3073	5.9204	2.0217	0.0858	0.0713	0.3055	-0.3729	-0.0948	-0.3401	-0.9326	-0.5941	-0.0079	0.4657	0.0226	0.0146	0.1421	0.0385	0.2115	39.021	26.566	96.461
14	2.127	-1.2551	-0.9126	5.1598	3.0631	3.8922	-0.1047	-0.1871	0.5924	-0.4746	0.3082	-0.4555	-0.7416	0.3311	-0.2655	0.3116	-0.0295	-0.0402	0.2137	-0.0432	0.2386	30.4	35.145	93.274
15	3.1251	0.3702	0.3499	5.4679	-1.0768	5.7765	0.0691	0.3609	-0.023	-0.6775	-0.0755	-0.2922	-0.0243	0.1336	0.0012	0.1812	0.0391	0.0369	0.1728	-0.016	0.0808	30.471	56.204	83.851
16	5.5431	0.5032	1.6951	8.2448	3.6334	6.3349	-0.1325	-0.0315	-0.1551	0.0417	0.349	-0.8572	0.1528	0.5467	-0.177	0.117	0.0092	-0.0044	0.2164	0.0078	0.133	21.177	54.413	95.657
17	3.7883	0.0641	-0.44	3.5035	0.0737	3.1393	-0.0762	-0.0724	-0.1275	-0.0446	0.0876	0.2504	0.1146	-0.2849	-0.0229	0.1424	-0.0181	0.0059	0.128	0.0243	0.061	38.448	47.943	97.35
18	1.7468	1.1724	1.8336	5.7345	3.9754	3.3362	-0.1279	0.0753	0.2549	-0.1917	-0.2833	0.5713	-0.1582	-0.2327	0.4139	0.1899	0.0317	0.0016	0.1146	0.0143	0.1403	45.228	43.462	91.071
19	5.9813	2.563	-0.5597	6.7256	0.5635	3.8652	0.1128	-0.5915	-0.1187	0.7672	-0.1423	0.6706	0.0873	-0.6175	-0.0105	0.222	0.0206	0.0204	0.2938	0.0202	0.1592	43.408	40.066	105.984
20	4.0443	0.7914	-0.8225	5.6949	-2.1617	5.0873	-0.0669	-0.1839	-0.1036	0.0329	0.1133	0.851	0.1859	-0.5101	-0.0597	0.0892	-0.0048	0.0268	0.1873	-0.0075	0.1839	41.8422	14.6113	79.2061
21	6.3525	4.5409	4.4328	7.5327	6.1696	6.4083	-0.0087	-0.0265	0.3086	-0.1379	0.263	-0.5618	-0.3135	0.3378	-0.1973	0.1359	-0.005	0.0048	0.118	0.0244	0.2188	56.5935	31.8688	80.5954
22	4.5617	0.3474	-0.0035	4.4254	-0.3357	2.4729	-0.0244	0.2093	-0.2029	-0.2948	0.0321	-0.2881	0.2845	0.0865	-0.01	0.1202	0.0073	0.0354	0.1212	-0.0192	0.091	55.9094	4.7331	75.3027
23	4.1198	0.0165	-0.1062	4.2403	-0.0383	2.5228	-0.022	-0.2771	-0.2211	0.3622	0.0407	-0.5405	0.1893	0.2862	0.0082	0.1059	0.0238	-0.03	0.1548	-0.0005	0.1728	59.8855	9.3988	82.3337
24	5.045	3.8345	-0.6319	6.4455	-0.7184	0.7967	0.204	-0.5459	-0.0002	1.2086	-0.0991	-0.198	-0.037	0.0601	-0.0637	0.321	0.0451	-0.0009	0.2013	-0.0223	0.1681	54.8502	20.7696	91.3203
25	2.7118	1.3124	1.1988	9.5895	4.5918	5.6007	0.0006	-0.1219	-0.0836	0.1407	0.1871	-1.1002	-0.0799	0.4406	-0.143	0.1606	-0.0075	-0.0296	0.1815	0.0379	0.1819	38.8515	49.2026	38.6751
26	5.2462	3.7919	-2.6006	5.7243	-3.3125	4.6107	0.0091	-0.1986	-0.5287	0.0038	0.2204	0.6405	0.7375	-0.3613	-0.146	0.3065	-0.0195	0.0023	0.1715	0.0701	0.4812	24.2355	31.7238	38.119
27	4.0515	-3.1335	-1.3316	8.3839	3.0128	2.3526	0.0204	0.0962	0.1211	-0.3859	-0.0887	0.043	-0.3783	0.0104	0.0678	0.1417	-0.0071	-0.0304	0.1408	0.0128	0.0611	28.8726	60.063	34.2764
28	4.47	-0.0692	0.6196	4.6611	-0.9575	4.3914	-0.0915	0.3575	0.332	-0.5416	-0.2182	1.0094	-0.447	-0.6132	0.0494	0.207	0.0634	-0.082	0.3246	-0.0087	0.346	14.6509	58.6303	31.1822
29	5.5216	-0.2287	0.0985	5.1547	-0.0703	4.5139	0.0292	-0.5423	0.1756	0.7387	0.0108	0.4805	-0.296	-0.5355	0.107	0.1964	0.0222	0.0528	0.1951	0.0262	0.1714	20.2616	53.3804	42.9852
30	3.711	1.7895	0.7213	4.8773	0.4999	1.38	0.0147	-0.7164	-0.3273	0.9867	0.0821	0.3314	0.2588	-0.1829	-0.0661	0.3374	0.0298	0.0369	0.2753	0.1088	0.2109	24.7325	42.8861	47.3271

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 67 through 89 )	A	67 - 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 131 )	A	109 - 131
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 132 through 162 )	A	132 - 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 204 )	A	187 - 204
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 205 through 218 )	A	205 - 218
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 219 through 232 )	A	219 - 232
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 240 through 252 )	A	240 - 252
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 253 through 275 )	A	253 - 275
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 276 through 301 )	A	276 - 301
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 67 through 89 )	B	67 - 89
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 90 through 107 )	B	90 - 107
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 108 through 131 )	B	108 - 131
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 132 through 162 )	B	132 - 162
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 163 through 186 )	B	163 - 186
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 187 through 252 )	B	187 - 252
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 253 through 272 )	B	253 - 272
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 273 through 298 )	B	273 - 298
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 67 through 89 )	C	67 - 89
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 90 through 125 )	C	90 - 125
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 126 through 175 )	C	126 - 175
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 176 through 230 )	C	176 - 230
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 231 through 287 )	C	231 - 287
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 66 through 89 )	D	66 - 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 162 )	D	126 - 162
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 163 through 186 )	D	163 - 186
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 187 through 218 )	D	187 - 218
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 219 through 287 )	D	219 - 287

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