PDB-5hk2: Human sigma-1 receptor bound to 4-IBP

ID or keywords:

Entry

Database: PDB / ID: 5hk2

Title

Human sigma-1 receptor bound to 4-IBP

Components

Sigma non-opioid intracellular receptor 1

Keywords

MEMBRANE PROTEIN /

Sigma-1 receptor /

transmembrane receptor /

ligand / trimer

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 /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Schmidt, H.R. / Zheng, S. / Gurpinar, E.G. / 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	Nov 22, 2017	Group: Database references / Derived calculations / Refinement description Category: citation / pdbx_struct_oper_list / software Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5hk2.cif.gz	272.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5hk2.ent.gz	221.6 KB	Display	PDB format
PDBx/mmJSON format	5hk2.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hk/5hk2 ftp://data.pdbj.org/pub/pdb/validation_reports/hk/5hk2	HTTPS FTP

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Related structure data

Related structure data	5hk1SC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5hk1-d 6dk1-d 6djz-d 6dk0-d 6qpw-d 22600 2y3a-d 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

81.3 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)	85.700, 126.800, 110.800
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

#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-61V / N-(1-benzylpiperidin-4-yl)-4-iodobenzamide Mass: 420.287 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₉H₂₁IN₂O
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 12 / 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

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.94 Å³/Da / Density % sol: 68.8 %
Crystal grow	Temperature: 293 K / Method: lipidic cubic phase / pH: 6.5 Details: Reconstituted in 10:1 monoolein: cholesterol mix. Precipitant solution: 30-40% PEG 300, 220-250 mM lithium sulfide, 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: 3.2→50 Å / Num. obs: 19968 / % possible obs: 97.1 % / Redundancy: 3.2 % / R_merge(I) obs: 0.194 / Net I/σ(I): 5.8
Reflection shell	Resolution: 3.2→3.3 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.897 / Mean I/σ(I) obs: 1.9 / % possible all: 97.8

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XSCALE		data scaling
Coot		model building
SHARP		phasing
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HK1

5hk1

Resolution: 3.2→33.604 Å / SU ML: 0.43 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 26.91 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.261	1998	10.01 %
R_work	0.2182	-	-
obs	0.2225	19968	97.28 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.2→33.604 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5027	0	199	0	5226

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	5359
X-RAY DIFFRACTION	f_angle_d	0.613	7304
X-RAY DIFFRACTION	f_dihedral_angle_d	13.246	1811
X-RAY DIFFRACTION	f_chiral_restr	0.024	797
X-RAY DIFFRACTION	f_plane_restr	0.003	897

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 (%)
3.2001-3.28	0.3973	140	0.3325	1264	X-RAY DIFFRACTION	98
3.28-3.3686	0.3486	141	0.2966	1254	X-RAY DIFFRACTION	97
3.3686-3.4676	0.337	141	0.2952	1273	X-RAY DIFFRACTION	98
3.4676-3.5795	0.3037	144	0.2509	1294	X-RAY DIFFRACTION	98
3.5795-3.7072	0.3023	140	0.2301	1268	X-RAY DIFFRACTION	99
3.7072-3.8555	0.2733	141	0.2315	1266	X-RAY DIFFRACTION	98
3.8555-4.0307	0.3078	142	0.2154	1276	X-RAY DIFFRACTION	98
4.0307-4.2428	0.2333	143	0.1974	1281	X-RAY DIFFRACTION	98
4.2428-4.508	0.2129	144	0.1887	1295	X-RAY DIFFRACTION	98
4.508-4.8551	0.2147	141	0.1767	1279	X-RAY DIFFRACTION	98
4.8551-5.342	0.2063	144	0.1759	1295	X-RAY DIFFRACTION	98
5.342-6.1109	0.2687	144	0.2063	1297	X-RAY DIFFRACTION	97
6.1109-7.6839	0.2686	146	0.2219	1303	X-RAY DIFFRACTION	96
7.6839-33.6054	0.2265	147	0.2136	1325	X-RAY DIFFRACTION	93

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	2.5554	0.2771	-1.5221	0.7029	0.7715	2.1947	0.4595	0.2039	0.0769	-0.9303	-0.6361	0.2452	0.281	-0.5564	0.2506	1.2375	0.1471	-0.0912	0.567	0.1442	0.5028	-3.1767	5.0403	15.45
2	0.88	-0.2986	-0.8006	3.8293	-0.6193	0.9403	-0.2252	-0.4647	-0.9111	0.3877	0.0885	0.9551	0.3383	-0.4721	0.0141	0.6828	-0.1608	0.1657	0.7314	0.2177	0.9687	-18.8625	13.6374	-26.292
3	3.934	-0.7244	-0.086	1.8313	0.5423	0.2245	0.2171	-0.6389	-0.5554	0.0206	-0.1887	-0.0645	0.2515	-0.0415	-0.0242	0.5076	-0.0081	0.0016	0.5445	0.2043	0.7152	-4.1059	17.9943	-30.7225
4	1.8756	-0.167	-0.0942	0.7853	0.9712	1.355	-0.1954	-0.8012	-0.8854	0.2866	-0.0292	-0.0271	0.1068	0.3373	0.2593	0.6902	-0.0172	0.1095	0.7812	0.206	0.5706	-14.0282	24.2803	-21.6856
5	1.0979	-0.432	0.8202	0.8586	1.6188	6.8454	0.6284	-0.7654	-0.1958	0.7206	-0.0166	-0.0223	1.393	-0.0194	-0.7605	0.8314	-0.1211	-0.1834	0.6572	0.3591	0.7068	-36.5601	59.8588	-13.1088
6	2.7353	-2.401	0.0923	6.9431	4.2149	4.6952	-0.1215	-0.2416	-0.197	-0.5234	-0.1199	0.7178	-0.4877	-0.1934	0.1288	0.4272	-0.0719	-0.072	0.3624	0.0982	0.4392	-23.2572	53.7773	-50.2997
7	2.4566	0.028	-0.213	2.5302	0.3734	1.2464	0.0102	-0.0276	0.0271	0.13	-0.0495	0.12	0.0534	-0.2125	0.0753	0.3338	-0.0308	0.0415	0.3944	-0.0192	0.3082	-15.4847	47.7071	-39.1222
8	4.6799	-0.4053	-3.1768	0.784	0.8733	4.9554	1.1193	-0.8627	0.5354	0.7706	-0.1495	-0.1313	0.6454	-0.7451	-0.9338	0.9099	-0.3883	-0.1147	0.7236	0.0829	0.771	28.8005	59.2558	-17.661
9	5.6725	4.6464	4.8477	4.4946	5.8657	9.3868	-0.2076	0.1284	0.401	-0.795	-0.0793	-0.4118	-0.8246	0.2629	0.1818	0.5348	0.0383	0.0065	0.4283	0.1016	0.5634	24.492	36.9536	-45.9009
10	2.5345	0.3417	-0.1519	5.5913	-0.5103	4.9227	0.083	-0.2311	-0.3063	0.3326	0.0412	-0.8123	0.3445	0.2623	-0.1187	0.3883	0.0906	-0.1438	0.5339	0.0416	0.6482	26.0404	27.552	-38.5493
11	3.9051	-2.389	-0.8085	3.6017	-0.0302	1.4774	-0.2315	-0.2449	0.2264	0.3173	0.1464	-0.1552	-0.1288	-0.07	0.1078	0.2876	0.0145	0.0027	0.3442	-0.0269	0.2862	10.4405	36.4833	-38.7923
12	2.6129	-2.1289	-0.7398	4.3666	1.2822	0.4035	0.2831	0.5228	0.1961	-0.3731	-0.487	-0.292	-0.0696	-0.0964	0.4159	0.6482	0.0142	0.0611	0.5013	0.0694	0.4488	6.6444	42.8475	-48.9183
13	0.531	-0.0405	-0.6472	1.8183	-0.1109	2.2811	0.092	-0.0585	-0.1004	0.472	0.0722	-0.2289	-0.2488	0.1721	-0.2753	0.4873	0.029	-0.1342	0.4541	-0.0084	0.3482	14.516	35.7466	-30.433

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 32 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 33 through 98 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 99 through 159 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 160 through 218 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 31 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 32 through 68 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 69 through 220 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 8 through 31 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 32 through 53 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 54 through 80 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 81 through 137 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 138 through 159 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 160 through 219 )

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