PDB-5hk1: Human sigma-1 receptor bound to PD144418

ID or keywords:

Entry

Database: PDB / ID: 5hk1

Title

Human sigma-1 receptor bound to PD144418

Components

Sigma non-opioid intracellular receptor 1

Keywords

MEMBRANE PROTEIN /

sigma-1 receptor /

transmembrane receptor /

signal transduction

Function / homology

Function and homology information

G protein-coupled opioid receptor activity / nuclear outer membrane / anchoring junction / lipid transport / nuclear inner membrane / protein homotrimerization / regulation of neuron apoptotic process /

lipid droplet / postsynaptic density membrane /

nuclear envelope ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SIRAS / Resolution: 2.5051 Å

Authors

Schmidt, H.R. / Zheng, S. / Gurpinar, E. / Koehl, A. / Manglik, A. / Kruse, A.C.

Citation

Journal: Nature / Year: 2016
Title: Crystal structure of the human sigma 1 receptor.
Authors: Schmidt, H.R. / Zheng, S. / Gurpinar, E. / Koehl, A. / Manglik, A. / Kruse, A.C.

History

Deposition	Jan 13, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 6, 2016	Provider: repository / Type: Initial release
Revision 1.1	Apr 20, 2016	Group: Database references
Revision 1.2	May 11, 2016	Group: Database references
Revision 1.3	Mar 6, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5hk1.cif.gz	281.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5hk1.ent.gz	228.6 KB	Display	PDB format
PDBx/mmJSON format	5hk1.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/hk/5hk1 ftp://data.pdbj.org/pub/pdb/validation_reports/hk/5hk1	HTTPS FTP

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Related structure data

Related structure data	5hk2C C: citing same article (ref.)
Similar structure data	6djz-d 6dk1-d 6dk0-d 5hk2-d 6qpw-d 22600 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
Related items in Molecule of the Month	#217 - Jan 2018 Opioid Receptors similarity (1) #164 - Aug 2013 Serotonin Receptor similarity (1) #199 - Jul 2016 Monellin similarity (1) #208 - Apr 2017 Glucose Transporters similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1)

Deposited unit

A: Sigma non-opioid intracellular receptor 1

B: Sigma non-opioid intracellular receptor 1

C: Sigma non-opioid intracellular receptor 1

hetero molecules

81 kDa, 3 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)	85.556, 126.062, 109.702
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	C-304- SO4

#1: Protein	Sigma non-opioid intracellular receptor 1 / Aging-associated gene 8 protein / SR31747-binding protein / SR-BP / Sigma 1-type opioid receptor / hSigmaR1 Mass: 25447.879 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SIGMAR1, OPRS1, SRBP, AAG8 / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99720
#2: Chemical	ChemComp-61W / 3-(4-methylphenyl)-5-(1-propyl-3,6-dihydro-2H-pyridin-5-yl)-1,2-oxazole / PD144418 / PD 144418 Mass: 282.380 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₈H₂₂N₂O
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol Mass: 356.540 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂₁H₄₀O₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.87 Å³/Da / Density % sol: 68.25 %
Crystal grow	Temperature: 293 K / Method: lipidic cubic phase / pH: 6.5 Details: Reconstituted in 10:1 monoolein:cholesterol mix. Precipitant solution: 40-50% PEG 300, 220-250 mM lithium sulfoxide, 0.1 M MES pH 6.5.

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Data collection

Diffraction	Mean temperature: 80 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.033 Å / Relative weight: 1
Reflection	Resolution: 2.5→40 Å / Num. obs: 41033 / % possible obs: 98.8 % / Redundancy: 3.46 % / R_sym value: 0.075 / Net I/σ(I): 10.1
Reflection shell	Resolution: 2.5→2.65 Å / Redundancy: 3.38 % / Mean I/σ(I) obs: 0.9 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Coot		model building
SHARP		phasing

Refinement

Method to determine structure:

SIRAS / Resolution: 2.5051→40 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2326	2000	4.87 %
R_work	0.1951	-	-
obs	0.197	41026	98.84 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.5051→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5097	0	213	160	5470

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5446
X-RAY DIFFRACTION	f_angle_d	0.586	7429
X-RAY DIFFRACTION	f_dihedral_angle_d	13.175	1801
X-RAY DIFFRACTION	f_chiral_restr	0.021	804
X-RAY DIFFRACTION	f_plane_restr	0.003	909

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 (%)
2.5051-2.5677	0.3672	136	0.3511	2647	X-RAY DIFFRACTION	95
2.5677-2.6371	0.3087	140	0.3209	2744	X-RAY DIFFRACTION	100
2.6371-2.7147	0.3465	142	0.3108	2771	X-RAY DIFFRACTION	100
2.7147-2.8023	0.3593	142	0.2993	2782	X-RAY DIFFRACTION	99
2.8023-2.9025	0.3018	142	0.2685	2764	X-RAY DIFFRACTION	99
2.9025-3.0187	0.3332	142	0.2392	2753	X-RAY DIFFRACTION	99
3.0187-3.156	0.2721	143	0.2135	2800	X-RAY DIFFRACTION	100
3.156-3.3224	0.2411	143	0.202	2793	X-RAY DIFFRACTION	100
3.3224-3.5305	0.2318	142	0.1754	2785	X-RAY DIFFRACTION	99
3.5305-3.8029	0.2031	144	0.1652	2792	X-RAY DIFFRACTION	99
3.8029-4.1854	0.2227	144	0.1749	2804	X-RAY DIFFRACTION	99
4.1854-4.7905	0.1917	143	0.1615	2807	X-RAY DIFFRACTION	98
4.7905-6.0334	0.2294	147	0.1848	2848	X-RAY DIFFRACTION	99
6.0334-46.1839	0.2077	150	0.1928	2936	X-RAY DIFFRACTION	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	1.8835	0.2124	-0.0066	0.207	-1.068	6.183	0.9496	-0.6899	-0.2779	0.6505	-0.2365	0.0085	0.4857	-0.5699	-0.6908	0.9252	-0.3081	-0.0659	0.9137	0.1354	0.9607	28.5668	59.1178	-17.035
2	3.291	0.7478	1.7925	4.6573	2.42	3.6325	-0.2998	0.2939	0.053	-0.1824	0.3738	-0.3207	-0.1164	0.47	-0.1109	0.6401	0.0725	-0.0173	0.678	0.06	0.6738	24.606	31.8582	-44.1109
3	2.1722	0.3301	-0.5037	2.1089	-0.3781	1.4287	-0.1817	-0.1553	-0.0996	0.507	0.2707	-0.3662	-0.0337	0.2108	-0.0488	0.5214	0.0604	-0.0964	0.579	-0.0581	0.539	14.3101	33.4665	-34.3399
4	2.9623	0.6051	0.4234	0.2159	0.3137	1.6642	-0.2568	0.4117	0.3109	-0.1119	0.095	0.0286	0.1184	0.1666	0.2015	0.5538	0.0375	0.03	0.5012	-0.0284	0.6444	7.6097	40.6198	-47.3988
5	1.175	-0.2718	0.1238	1.3968	-0.0689	1.254	0.0081	-0.3631	-0.1524	0.4077	0.056	-0.2181	0.0604	-0.0268	-0.013	0.6025	0.0524	-0.0289	0.5768	-0.0309	0.4931	8.078	36.3322	-34.3882
6	8.0857	3.4253	-0.1498	4.2635	-0.094	2.7995	-0.1968	-0.5046	-0.059	0.4742	0.173	-0.5156	-0.1592	-0.1898	0.0444	0.7648	0.12	-0.2384	0.7098	-0.16	0.5334	21.7714	33.5518	-24.1017
7	5.1677	-1.3637	1.019	7.2005	-1.5213	6.8522	0.523	-0.2578	0.2472	-0.4573	-0.6433	-0.0086	-0.2697	-0.1264	0.1838	0.9211	0.0106	0.0754	0.8885	-0.0505	0.8675	-3.1069	4.2067	21.8149
8	2.537	-0.06	-0.3926	2.0662	-0.1985	1.7179	-0.1419	-0.5175	-0.6984	0.3662	0.1735	0.261	0.3588	-0.2182	-0.0611	0.747	-0.0249	0.0933	0.6543	0.1966	0.682	-12.5427	17.4771	-25.3515
9	2.9957	-1.2303	-2.029	2.4698	2.5186	8.5565	1.1786	-1.0137	0.2347	1.8953	-0.1028	-1.2474	1.4086	0.8494	-0.9298	1.5614	-0.3091	-0.2383	0.9885	0.166	0.9752	-36.7597	59.2463	-8.9444
10	2.9273	-0.7385	-1.2517	4.3778	2.6404	5.5025	0.0592	-0.1161	-0.0444	-0.3478	0.0203	0.5314	-0.2644	-0.6287	-0.0284	0.5711	0.0087	-0.1026	0.7377	0.1094	0.6965	-23.1591	53.6351	-49.7291
11	1.0908	-0.7659	-0.1696	2.6204	0.7764	1.4244	-0.0441	-0.0931	0.0795	0.1493	0.1025	0.168	0.065	-0.0941	-0.0737	0.4898	-0.0337	0.0063	0.5771	-0.0202	0.5257	-15.4253	47.3839	-38.7753

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 68 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 69 through 121 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 122 through 159 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 160 through 195 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 196 through 219 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 25 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 26 through 219 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 2 through 31 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 32 through 68 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 69 through 220 )

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