+Open data
-Basic information
Entry | Database: PDB / ID: 6dk0 | |||||||||
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Title | Human sigma-1 receptor bound to NE-100 | |||||||||
Components | Sigma non-opioid intracellular receptor 1 | |||||||||
Keywords | MEMBRANE PROTEIN / Antagonist bound / Receptor / sigma-1 receptor | |||||||||
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 ...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 / nervous system development / growth cone / cytoplasmic vesicle / Potential therapeutics for SARS / postsynaptic density / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | |||||||||
Authors | Schmidt, H.R. / Kruse, A.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dk0.cif.gz | 151.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dk0.ent.gz | 116.4 KB | Display | PDB format |
PDBx/mmJSON format | 6dk0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/6dk0 ftp://data.pdbj.org/pub/pdb/validation_reports/dk/6dk0 | HTTPS FTP |
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-Related structure data
Related structure data | 6djzC 6dk1C 5hk1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | 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 | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-OLC / ( #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.25 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2017 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.9→3 Å / Mean I/σ(I) obs: 0.5 / CC1/2: 0.24 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→46.176 Å
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Refine LS restraints |
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LS refinement shell |
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