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

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Basic information

Entry
Database: PDB / ID: 5hk1
TitleHuman sigma-1 receptor bound to PD144418
ComponentsSigma non-opioid intracellular receptor 1
KeywordsMEMBRANE 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 / nuclear inner membrane / lipid transport / protein homotrimerization / regulation of neuron apoptotic process / lipid droplet / postsynaptic density membrane / nuclear envelope ...G protein-coupled opioid receptor activity / nuclear outer membrane / anchoring junction / nuclear inner membrane / lipid transport / protein homotrimerization / regulation of neuron apoptotic process / lipid droplet / postsynaptic density membrane / nuclear envelope / nervous system development / growth cone / cytoplasmic vesicle / Potential therapeutics for SARS / postsynaptic density / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / membrane / cytosol
Similarity search - Function
ERG2/sigma1 receptor-like / ERG2 and Sigma1 receptor like protein
Similarity search - Domain/homology
Chem-61W / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Sigma non-opioid intracellular receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.5051 Å
AuthorsSchmidt, H.R. / Zheng, S. / Gurpinar, E. / Koehl, A. / Manglik, A. / Kruse, A.C.
CitationJournal: 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
DepositionJan 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Mar 6, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,03127
Polymers76,3443
Non-polymers4,68824
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-169 kcal/mol
Surface area30720 Å2
MethodPISA
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 number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-304-

SO4

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Components

#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


Mass: 282.380 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H22N2O
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 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

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 41033 / % possible obs: 98.8 % / Redundancy: 3.46 % / Rsym value: 0.075 / Net I/σ(I): 10.1
Reflection shellResolution: 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
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Cootmodel building
SHARPphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2326 2000 4.87 %
Rwork0.1951 --
obs0.197 41026 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5051→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5097 0 213 160 5470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025446
X-RAY DIFFRACTIONf_angle_d0.5867429
X-RAY DIFFRACTIONf_dihedral_angle_d13.1751801
X-RAY DIFFRACTIONf_chiral_restr0.021804
X-RAY DIFFRACTIONf_plane_restr0.003909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5051-2.56770.36721360.35112647X-RAY DIFFRACTION95
2.5677-2.63710.30871400.32092744X-RAY DIFFRACTION100
2.6371-2.71470.34651420.31082771X-RAY DIFFRACTION100
2.7147-2.80230.35931420.29932782X-RAY DIFFRACTION99
2.8023-2.90250.30181420.26852764X-RAY DIFFRACTION99
2.9025-3.01870.33321420.23922753X-RAY DIFFRACTION99
3.0187-3.1560.27211430.21352800X-RAY DIFFRACTION100
3.156-3.32240.24111430.2022793X-RAY DIFFRACTION100
3.3224-3.53050.23181420.17542785X-RAY DIFFRACTION99
3.5305-3.80290.20311440.16522792X-RAY DIFFRACTION99
3.8029-4.18540.22271440.17492804X-RAY DIFFRACTION99
4.1854-4.79050.19171430.16152807X-RAY DIFFRACTION98
4.7905-6.03340.22941470.18482848X-RAY DIFFRACTION99
6.0334-46.18390.20771500.19282936X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.88350.2124-0.00660.207-1.0686.1830.9496-0.6899-0.27790.6505-0.23650.00850.4857-0.5699-0.69080.9252-0.3081-0.06590.91370.13540.960728.566859.1178-17.035
23.2910.74781.79254.65732.423.6325-0.29980.29390.053-0.18240.3738-0.3207-0.11640.47-0.11090.64010.0725-0.01730.6780.060.673824.60631.8582-44.1109
32.17220.3301-0.50372.1089-0.37811.4287-0.1817-0.1553-0.09960.5070.2707-0.3662-0.03370.2108-0.04880.52140.0604-0.09640.579-0.05810.53914.310133.4665-34.3399
42.96230.60510.42340.21590.31371.6642-0.25680.41170.3109-0.11190.0950.02860.11840.16660.20150.55380.03750.030.5012-0.02840.64447.609740.6198-47.3988
51.175-0.27180.12381.3968-0.06891.2540.0081-0.3631-0.15240.40770.056-0.21810.0604-0.0268-0.0130.60250.0524-0.02890.5768-0.03090.49318.07836.3322-34.3882
68.08573.4253-0.14984.2635-0.0942.7995-0.1968-0.5046-0.0590.47420.173-0.5156-0.1592-0.18980.04440.76480.12-0.23840.7098-0.160.533421.771433.5518-24.1017
75.1677-1.36371.0197.2005-1.52136.85220.523-0.25780.2472-0.4573-0.6433-0.0086-0.2697-0.12640.18380.92110.01060.07540.8885-0.05050.8675-3.10694.206721.8149
82.537-0.06-0.39262.0662-0.19851.7179-0.1419-0.5175-0.69840.36620.17350.2610.3588-0.2182-0.06110.747-0.02490.09330.65430.19660.682-12.542717.4771-25.3515
92.9957-1.2303-2.0292.46982.51868.55651.1786-1.01370.23471.8953-0.1028-1.24741.40860.8494-0.92981.5614-0.3091-0.23830.98850.1660.9752-36.759759.2463-8.9444
102.9273-0.7385-1.25174.37782.64045.50250.0592-0.1161-0.0444-0.34780.02030.5314-0.2644-0.6287-0.02840.57110.0087-0.10260.73770.10940.6965-23.159153.6351-49.7291
111.0908-0.7659-0.16962.62040.77641.4244-0.0441-0.09310.07950.14930.10250.1680.065-0.0941-0.07370.4898-0.03370.00630.5771-0.02020.5257-15.425347.3839-38.7753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 121 )
4X-RAY DIFFRACTION4chain 'A' and (resid 122 through 159 )
5X-RAY DIFFRACTION5chain 'A' and (resid 160 through 195 )
6X-RAY DIFFRACTION6chain 'A' and (resid 196 through 219 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 25 )
8X-RAY DIFFRACTION8chain 'B' and (resid 26 through 219 )
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 31 )
10X-RAY DIFFRACTION10chain 'C' and (resid 32 through 68 )
11X-RAY DIFFRACTION11chain 'C' and (resid 69 through 220 )

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