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Yorodumi- PDB-5osc: GLIC-GABAAR alpha1 chimera crystallized in complex with pregnenol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5osc | |||||||||||||||
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Title | GLIC-GABAAR alpha1 chimera crystallized in complex with pregnenolone sulfate at pH 4.5 | |||||||||||||||
Components | Proton-gated ion channel,Gamma-aminobutyric acid receptor subunit alpha-2,Gamma-aminobutyric acid receptor subunit alpha-1 | |||||||||||||||
Keywords | TRANSPORT PROTEIN / GABAA-receptor ion channel Ion transport Extracellular ligand gated ion channel | |||||||||||||||
Function / homology | Function and homology information : / : / : / GABA receptor activation / diazepam binding / benzodiazepine receptor activity / inhibitory synapse / GABA receptor complex / organic cyclic compound binding / inhibitory extracellular ligand-gated monoatomic ion channel activity ...: / : / : / GABA receptor activation / diazepam binding / benzodiazepine receptor activity / inhibitory synapse / GABA receptor complex / organic cyclic compound binding / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA-gated chloride ion channel activity / cellular response to histamine / inhibitory synapse assembly / GABA-A receptor activity / GABA-A receptor complex / sodium channel activity / neurotransmitter transport / neurotransmitter receptor activity / postsynaptic specialization membrane / nervous system process / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / extracellular ligand-gated monoatomic ion channel activity / plasma membrane => GO:0005886 / chloride channel complex / potassium channel activity / GABA-ergic synapse / regulation of postsynaptic membrane potential / chloride transmembrane transport / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / regulation of membrane potential / monoatomic ion transmembrane transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cytoplasmic vesicle membrane / transmembrane signaling receptor activity / chemical synaptic transmission / postsynapse / neuron projection / axon / dendrite / neuronal cell body / synapse / signal transduction / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Gloeobacter violaceus (bacteria) Mus musculus (house mouse) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å | |||||||||||||||
Authors | Laverty, D.C. / Gold, M.G. / Smart, T.G. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: Crystal structures of a GABAA-receptor chimera reveal new endogenous neurosteroid-binding sites. Authors: Laverty, D. / Thomas, P. / Field, M. / Andersen, O.J. / Gold, M.G. / Biggin, P.C. / Gielen, M. / Smart, T.G. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5osc.cif.gz | 663.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5osc.ent.gz | 559.6 KB | Display | PDB format |
PDBx/mmJSON format | 5osc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/5osc ftp://data.pdbj.org/pub/pdb/validation_reports/os/5osc | HTTPS FTP |
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-Related structure data
Related structure data | 5osaSC 5osbC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 38644.180 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus (strain PCC 7421) (bacteria), (gene. exp.) Mus musculus (house mouse) Strain: PCC 7421 / Gene: glvI, glr4197, Gabra2, Gabra-2, Gabra1, Gabra-1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q7NDN8, UniProt: P26048, UniProt: P62812 #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-A8W / #5: Chemical | ChemComp-Y01 / |
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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: 4.99 Å3/Da / Density % sol: 75.34 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 12-16% PEG 4000, 100 mM NaCl, 100 mM Li2S04, 100 mM sodium acetate pH 4-5 PH range: 4-5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.97→83.52 Å / Num. obs: 77782 / % possible obs: 99.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 81.11 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 1 |
Reflection shell | Resolution: 2.97→3.05 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5OSA Resolution: 3.1→29.92 Å / SU ML: 0.434 / Cross valid method: FREE R-VALUE / σ(F): 1.343 / Phase error: 33.066
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 114.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.1→29.92 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 12.0503 Å / Origin y: -21.0137 Å / Origin z: 184.8753 Å
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Refinement TLS group | Selection details: ALL |