PDB-8wue: The sigma-1 receptor from Xenopus laevis in complex with dehydroe...

ID or keywords:

Entry

Database: PDB / ID: 8wue

Title

The sigma-1 receptor from Xenopus laevis in complex with dehydroepiandrosterone sulfate by soaking (C2 form)

Components

Sigma non-opioid intracellular receptor 1

Keywords

MEMBRANE PROTEIN / sigma receptor / S1R / endogenous ligand / neurosteroid / DHEAS

Function / homology

Function and homology information

nuclear inner membrane / lipid transport / nuclear outer membrane / cytoplasmic vesicle / endoplasmic reticulum membrane / endoplasmic reticulum / membrane
Similarity search - Function

Biological species

Xenopus laevis (African clawed frog)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.089 Å

Authors

Fu, C. / Sun, Z. / Zhou, X.

Funding support

China, 1items

Citation

Journal: Nat Commun / Year: 2024
Title: Insight into binding of endogenous neurosteroid ligands to the sigma-1 receptor.
Authors: Fu, C. / Xiao, Y. / Zhou, X. / Sun, Z.

History

Deposition	Oct 20, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 17, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8wue.cif.gz	538.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8wue.ent.gz	452.1 KB	Display	PDB format
PDBx/mmJSON format	8wue.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/wu/8wue ftp://data.pdbj.org/pub/pdb/validation_reports/wu/8wue	HTTPS FTP

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Related structure data

Related structure data	8w4bC 8w4cC 8w4dC 8w4eC 8wwbC 8ybbC 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: Sigma non-opioid intracellular receptor 1

B: Sigma non-opioid intracellular receptor 1

C: Sigma non-opioid intracellular receptor 1

D: Sigma non-opioid intracellular receptor 1

E: Sigma non-opioid intracellular receptor 1

F: Sigma non-opioid intracellular receptor 1

hetero molecules

157 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Sigma non-opioid intracellular receptor 1

B: Sigma non-opioid intracellular receptor 1

C: Sigma non-opioid intracellular receptor 1

hetero molecules

defined by author&software
Evidence: gel filtration
78.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Sigma non-opioid intracellular receptor 1

E: Sigma non-opioid intracellular receptor 1

F: Sigma non-opioid intracellular receptor 1

hetero molecules

defined by author&software
78.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.551, 144.665, 137.544
Angle α, β, γ (deg.)	90.00, 104.20, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Sigma non-opioid intracellular receptor 1 Mass: 25720.322 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: sigmar1 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q6DCU6
#2: Chemical	ChemComp-ZWY / 17-oxoandrost-5-en-3beta-yl hydrogen sulfate / Dehydroepiandrosterone sulfate / DHEA sulfate / DHEA-S Mass: 368.488 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₉H₂₈O₅S / Feature type: SUBJECT OF INVESTIGATION
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: 2.83 Å³/Da / Density % sol: 56.53 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.32M LiCl, 0.1M Na+-citrate pH 5.5, 12% PEG 4000, 10% glycerol, 15mM Na+-cholate, 1mM DHEAS soaking

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97853 Å / Relative weight: 1
Reflection	Resolution: 2.899→49.023 Å / Num. obs: 34345 / % possible obs: 90.2 % / Redundancy: 6 % / R_merge(I) obs: 0.111 / R_pim(I) all: 0.049 / R_rim(I) all: 0.121 / Net I/σ(I): 13.2 / Num. measured all: 206427
Reflection shell	Resolution: 2.899→2.979 Å / % possible obs: 58.3 % / Redundancy: 5.8 % / R_merge(I) obs: 1.57 / Num. measured all: 9918 / Num. unique obs: 1717 / R_pim(I) all: 0.706 / R_rim(I) all: 1.724 / Net I/σ(I) obs: 1.1

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
Aimless	0.7.4	data scaling
XDS	BUILT 20230630	data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.089→41.734 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.69 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2397	1541	4.89 %
R_work	0.2138	-	-
obs	0.215	31510	99.86 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.089→41.734 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10578	0	150	0	10728

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	11010
X-RAY DIFFRACTION	f_angle_d	0.626	14998
X-RAY DIFFRACTION	f_dihedral_angle_d	13.145	6202
X-RAY DIFFRACTION	f_chiral_restr	0.042	1702
X-RAY DIFFRACTION	f_plane_restr	0.003	1812

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 (%)
3.089-3.1885	0.286	157	0.2878	2705	X-RAY DIFFRACTION	100
3.1885-3.3024	0.3362	141	0.2809	2727	X-RAY DIFFRACTION	100
3.3024-3.4346	0.3118	145	0.2712	2694	X-RAY DIFFRACTION	100
3.4346-3.5908	0.2991	133	0.2225	2723	X-RAY DIFFRACTION	100
3.5908-3.78	0.2469	140	0.215	2713	X-RAY DIFFRACTION	100
3.78-4.0167	0.2266	119	0.2185	2750	X-RAY DIFFRACTION	100
4.0167-4.3265	0.2272	119	0.1993	2738	X-RAY DIFFRACTION	100
4.3265-4.7614	0.2293	158	0.1807	2719	X-RAY DIFFRACTION	100
4.7614-5.4491	0.2019	138	0.201	2706	X-RAY DIFFRACTION	100
5.4491-6.8603	0.24	159	0.2449	2734	X-RAY DIFFRACTION	100
6.8603-41.734	0.2187	132	0.1924	2760	X-RAY DIFFRACTION	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	6.1678	-1.5098	-3.9883	3.7384	-0.0152	7.8188	0.1044	-0.3694	-0.1162	-0.1184	-0.2137	-0.2427	0.6445	1.57	0.2779	0.2762	0.1052	-0.1288	0.6346	0.0183	0.7824	48.8298	29.2263	40.234
2	3.6156	0.2622	-1.2498	2.7112	-0.9886	5.8737	-0.0797	1.1162	0.4141	-0.7272	-0.0429	-0.285	-0.4382	-0.2172	0.147	0.8499	0.0911	-0.0611	1.061	0.163	0.5399	29.6083	40.3333	8.3731
3	1.446	-0.069	0.2002	2.3495	-2.0546	5.1622	-0.0206	0.3694	0.3497	-0.2537	-0.2209	-0.1511	-0.2307	0.1411	0.2436	0.555	0.1221	-0.0786	0.6775	0.0255	0.5791	31.5458	41.0418	22.4953
4	7.4222	-2.7352	-6.4955	2.2943	1.8332	5.8923	0.3227	1.6941	-0.1551	-0.6227	-0.5394	-0.1448	-0.1251	-1.0284	0.1995	0.9012	0.0725	-0.0745	1.154	-0.0096	0.4157	34.3361	25.7511	5.9906
5	5.625	-0.7061	5.6182	7.2714	0.3618	9.8178	0.5443	0.4692	-0.064	0.8656	-0.3966	1.0922	2.4495	0.3951	-0.2455	0.6315	0.1063	0.1729	0.5355	-0.04	0.5921	20.828	10.3658	45.9468
6	4.11	-1.3307	-0.2851	5.7224	0.3106	6.256	-0.1885	-0.5951	0.51	0.3981	-0.0521	-0.1801	-0.3507	0.5896	0.2546	0.5279	0.0342	-0.1817	0.6913	-0.0945	0.6322	36.3803	45.6249	53.0696
7	2.9688	2.3745	0.1584	2.491	0.7989	1.5002	0.0758	-0.4388	0.3975	0.3171	-0.2474	0.6717	-0.0178	-0.1653	0.1658	0.7287	0.1344	0.0008	0.7039	-0.0861	0.5637	24.1753	39.2581	49.4214
8	5.1941	1.2983	-1.0857	6.629	-0.9172	0.3839	0.2521	-0.4151	0.7053	0.4827	-0.2215	-0.4068	-0.2917	0.5028	-0.1019	0.5643	0.1724	-0.0676	0.6869	-0.0292	0.5517	42.5552	33.6376	46.4059
9	3.127	-0.8611	-1.4413	3.9214	0.26	3.9394	-0.1479	1.1718	-0.1903	-0.6588	-0.1867	0.7	-0.1184	-0.6321	0.3486	0.8881	0.1738	-0.086	0.8605	-0.202	0.6588	25.0838	12.8234	13.5091
10	5.4298	-3.6251	-4.1469	9.7507	5.5591	6.4526	0.0736	0.5521	-0.0098	-0.2461	-0.866	2.0382	-0.4046	-1.5844	0.7606	0.5614	0.0481	-0.1729	0.895	0.0271	1.1344	-4.6327	21.7621	30.8702
11	7.02	2.9461	-2.4815	7.3106	-0.7148	4.1394	0.3899	-0.1398	0.0326	0.587	-0.2405	0.8919	0.1118	-0.2849	-0.1493	0.5134	0.0963	-0.0082	0.7201	-0.071	0.7483	2.9099	22.1275	42.3362
12	2.2364	0.0184	-0.0951	2.5979	-1.5196	2.7416	0.2417	0.4453	-0.1175	0.0369	-0.1649	0.4806	-0.0513	-0.4608	-0.0676	0.5672	0.1123	-0.0353	0.662	-0.1271	0.6517	10.3481	23.2722	32.5438
13	7.5033	5.1902	5.5386	4.336	4.9595	5.704	0.1379	-0.5835	0.5473	0.8592	-0.6194	0.842	0.5604	-0.5803	0.3807	0.7852	0.0592	0.0415	0.7844	0.0458	0.6803	27.9894	2.3574	48.8045
14	7.3986	1.5529	-0.15	4.9968	1.5362	3.8829	-0.1099	1.2073	0.022	-0.3556	-0.0616	0.3159	0.7844	-0.0798	0.1704	0.9823	0.182	0.0085	1.0135	-0.0569	0.678	32.0955	-18.5121	17.2303
15	1.3019	-1.444	0.9956	3.264	-0.1027	3.3149	0.0275	0.3809	-0.3027	-0.0158	-0.2507	0.5785	0.4716	-0.2939	0.2399	0.666	0.1287	0.143	0.8967	-0.0387	0.8934	34.7413	-13.2543	26.381
16	4.073	-0.2377	-0.8005	7.982	-1.0783	8.4087	-0.5572	-0.0824	0.6646	0.0852	-0.1625	-0.4311	-1.0512	-0.3694	0.6804	0.7248	0.1832	-0.1276	0.796	0.0993	1.0006	54.3024	20.0332	36.5224
17	4.8607	1.5604	-1.4744	6.1851	-1.0529	5.122	0.0647	-0.8497	-0.6003	1.3286	-0.2187	-0.3348	0.8753	1.2898	0.103	1.0331	0.3792	0.1363	1.164	0.2683	0.68	49.8003	-11.6604	62.8378
18	1.4137	1.6154	-1.5587	3.1355	1.2982	8.864	-0.3118	-0.5006	0.0908	0.4048	-0.2368	0.5397	1.5387	0.3728	0.6101	0.8175	0.229	0.0882	0.7512	0.0812	0.8104	39.9795	-9.2952	54.4075
19	1.349	0.9122	-1.3949	1.3082	-0.566	1.6218	-0.0509	-0.2648	-0.0701	0.0951	-0.2731	-0.2564	0.2605	0.4434	0.3519	0.7954	0.2903	0.0557	0.6738	0.0937	0.7469	52.1633	-5.1556	47.8727
20	1.7709	-0.7116	-0.1257	1.9488	-0.724	2.0616	-0.7233	-0.1023	0.1338	0.5695	-0.4473	-0.2424	1.0379	0.2603	1.2886	1.0291	0.1966	0.1764	0.7885	0.0072	0.8387	33.9202	-1.4375	60.1087
21	2.3742	2.1144	-0.2921	6.8592	-4.1411	3.0195	1.1938	0.5725	-1.1006	0.9647	-0.5222	-0.1932	-1.1024	0.7072	-0.8194	1.2682	0.1373	-0.1289	1.0952	-0.1473	0.7223	37.0004	8.7076	11.2656
22	7.0137	-5.3958	6.899	5.0817	-6.5786	8.556	-0.1699	1.1128	-0.5835	-0.3503	-0.8624	-0.9066	-0.0879	1.9604	0.8369	0.9978	0.1935	0.3252	1.0603	0.3132	1.297	71.5821	3.2456	15.5689
23	8.3901	2.0878	-1.603	0.8925	0.5074	2.4836	-0.0255	0.0105	-0.2667	-0.0087	-0.1364	-0.0428	-0.2905	0.2236	0.2065	0.654	0.1315	0.0133	0.926	0.3151	0.9516	69.5452	6.5032	28.7205
24	2.0459	0.7942	-1.1503	2.9443	0.7331	1.107	0.08	0.5183	0.3259	-0.4951	-0.15	-0.5589	-0.1541	0.0169	0.067	0.7518	0.2672	0.0917	0.8706	0.2954	0.8357	58.8194	3.0274	23.9457

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -5 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 95 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 96 through 192 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 193 through 220 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -5 through 26 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 27 through 95 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 96 through 174 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 175 through 219 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid -5 through 25 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 26 through 50 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 51 through 95 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 96 through 219 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid -5 through 26 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 27 through 106 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 107 through 219 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid -5 through 26 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 27 through 65 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 66 through 95 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 96 through 192 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 193 through 220 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid -5 through 25 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 26 through 50 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 51 through 95 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 96 through 219 )

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