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- PDB-6djz: Human sigma-1 receptor bound to haloperidol -

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Basic information

Entry
Database: PDB / ID: 6djz
TitleHuman sigma-1 receptor bound to haloperidol
ComponentsSigma non-opioid intracellular receptor 1
KeywordsMEMBRANE PROTEIN / 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-GMJ / (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: 3.084 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)81,86833
Polymers76,3443
Non-polymers5,52530
Water54030
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 area9360 Å2
ΔGint-179 kcal/mol
Surface area29890 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 / Cell (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99720

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Non-polymers , 5 types, 60 molecules

#2: Chemical ChemComp-GMJ / 4-[4-(4-chlorophenyl)-4-hydroxypiperidin-1-yl]-1-(4-fluorophenyl)butan-1-one


Mass: 375.864 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H23ClFNO2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / 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.: 7 / Source method: obtained synthetically / Formula: C21H40O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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 / pH: 6.4
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 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 500 mM lithium sulfate, 42% PEG 300, 1% hexanediol, 100 mM MES pH 6.4

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.08→50 Å / Num. obs: 22196 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.994 / Net I/σ(I): 5.9
Reflection shellResolution: 3.08→3.3 Å / Redundancy: 5 % / Mean I/σ(I) obs: 0.4 / CC1/2: 0.164 / % possible all: 99.6

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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: 3.084→40.509 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.49
RfactorNum. reflection% reflection
Rfree0.2764 1901 4.84 %
Rwork0.2392 --
obs0.241 21454 93.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.084→40.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5021 0 242 30 5293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035391
X-RAY DIFFRACTIONf_angle_d0.4897358
X-RAY DIFFRACTIONf_dihedral_angle_d16.7392918
X-RAY DIFFRACTIONf_chiral_restr0.038795
X-RAY DIFFRACTIONf_plane_restr0.003901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0843-3.16140.4132420.4293855X-RAY DIFFRACTION29
3.1614-3.24690.42221180.40122260X-RAY DIFFRACTION79
3.2469-3.34240.38561430.37752776X-RAY DIFFRACTION97
3.3424-3.45020.37751450.35342844X-RAY DIFFRACTION99
3.4502-3.57340.38811530.33162884X-RAY DIFFRACTION100
3.5734-3.71640.34361390.32492869X-RAY DIFFRACTION100
3.7164-3.88540.34711450.29662851X-RAY DIFFRACTION100
3.8854-4.09010.28051530.26552884X-RAY DIFFRACTION100
4.0901-4.34610.29471440.22212852X-RAY DIFFRACTION100
4.3461-4.68120.21581410.18252864X-RAY DIFFRACTION100
4.6812-5.15140.22361460.17922864X-RAY DIFFRACTION100
5.1514-5.89490.23471440.19842860X-RAY DIFFRACTION100
5.8949-7.41950.27841430.22542877X-RAY DIFFRACTION100
7.4195-40.51260.23631450.21352854X-RAY DIFFRACTION99

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