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- PDB-6dk0: Human sigma-1 receptor bound to NE-100 -

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Basic information

Entry
Database: PDB / ID: 6dk0
TitleHuman sigma-1 receptor bound to NE-100
ComponentsSigma non-opioid intracellular receptor 1
KeywordsMEMBRANE PROTEIN / Antagonist bound / Receptor / sigma-1 receptor
Function / homology
Function and homology information


G protein-coupled opioid receptor activity / nuclear inner membrane / anchoring junction / lipid transport / protein homotrimerization / nuclear outer membrane / regulation of postsynapse assembly / regulation of neuron apoptotic process / lipid droplet / postsynaptic density membrane ...G protein-coupled opioid receptor activity / nuclear inner membrane / anchoring junction / lipid transport / protein homotrimerization / nuclear outer membrane / regulation of postsynapse assembly / 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 / glutamatergic synapse / 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-GKY / (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 / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSchmidt, H.R. / Kruse, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE1745303 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM119185 United States
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: Structural basis for sigma1receptor ligand recognition.
Authors: Schmidt, H.R. / Betz, R.M. / Dror, R.O. / Kruse, A.C.
History
DepositionMay 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: 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

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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)81,88431
Polymers76,3443
Non-polymers5,54028
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Multi-angle light scattering experiments (and others) indicate that sigma-1 recepto can adopt a variety of oligomerization states. The trimeric arrangement present in the ...Evidence: light scattering, Multi-angle light scattering experiments (and others) indicate that sigma-1 recepto can adopt a variety of oligomerization states. The trimeric arrangement present in the asymmetric unit shown here is likely representative of one particular biological oligomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-171 kcal/mol
Surface area30290 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

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Protein , 1 types, 3 molecules ABC

#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 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99720

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Non-polymers , 5 types, 124 molecules

#2: Chemical ChemComp-GKY / N-{2-[4-methoxy-3-(2-phenylethoxy)phenyl]ethyl}-N-propylpropan-1-amine


Mass: 355.514 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H33NO2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68.25 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: Protein was reconstituted in cubic phase by mixing with a 1:1.5 (w:w) protein:lipid ratio. Lipid used was a 10:1 (w:w) mix of monoolein with cholesterol. Crystals were grown in 400-500 mM ...Details: Protein was reconstituted in cubic phase by mixing with a 1:1.5 (w:w) protein:lipid ratio. Lipid used was a 10:1 (w:w) mix of monoolein with cholesterol. Crystals were grown in 400-500 mM lithium sulfate, 30-40% PEG 300, 1% hexanediol, 0.1 M MES pH 5.8-6.0
PH range: 5.8-6.0

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 25810 / % possible obs: 95.3 % / Redundancy: 7.2 % / CC1/2: 0.989 / Net I/σ(I): 5.6
Reflection shellResolution: 2.9→3 Å / Mean I/σ(I) obs: 0.5 / CC1/2: 0.24 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HK1

5hk1


Resolution: 2.9→46.176 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.85
RfactorNum. reflection% reflection
Rfree0.2733 2164 4.85 %
Rwork0.2505 --
obs0.2516 25243 85.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→46.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5052 0 233 96 5381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025412
X-RAY DIFFRACTIONf_angle_d0.4637369
X-RAY DIFFRACTIONf_dihedral_angle_d16.992950
X-RAY DIFFRACTIONf_chiral_restr0.037793
X-RAY DIFFRACTIONf_plane_restr0.003905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8799-2.94690.3884600.40161074X-RAY DIFFRACTION33
2.9469-3.02060.39831210.36512516X-RAY DIFFRACTION77
3.0206-3.10220.32311420.37012836X-RAY DIFFRACTION86
3.1022-3.19350.3931530.3462872X-RAY DIFFRACTION88
3.1935-3.29650.38031640.32883070X-RAY DIFFRACTION92
3.2965-3.41430.29911610.30483055X-RAY DIFFRACTION93
3.4143-3.5510.29491510.27693056X-RAY DIFFRACTION93
3.551-3.71250.31141530.26633021X-RAY DIFFRACTION92
3.7125-3.90820.27341630.27093031X-RAY DIFFRACTION92
3.9082-4.15290.28691490.24172982X-RAY DIFFRACTION92
4.1529-4.47330.22391430.21853033X-RAY DIFFRACTION91
4.4733-4.9230.21651550.19692917X-RAY DIFFRACTION89
4.923-5.63430.25111500.21393005X-RAY DIFFRACTION92
5.6343-7.09440.29391520.24283002X-RAY DIFFRACTION91
7.0944-46.1820.23641470.22422958X-RAY DIFFRACTION89

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