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- PDB-6m8r: Crystal structure of the KCTD16 BTB domain in complex with GABAB2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m8r | ||||||
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Title | Crystal structure of the KCTD16 BTB domain in complex with GABAB2 peptide | ||||||
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![]() | PROTEIN BINDING / pentamer / BTB domain | ||||||
Function / homology | ![]() GABA B receptor activation / G protein-coupled GABA receptor complex / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / GABA receptor complex / negative regulation of adenylate cyclase activity / regulation of G protein-coupled receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / synaptic transmission, GABAergic ...GABA B receptor activation / G protein-coupled GABA receptor complex / neuron-glial cell signaling / G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / GABA receptor complex / negative regulation of adenylate cyclase activity / regulation of G protein-coupled receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cell projection / protein homooligomerization / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / transmembrane signaling receptor activity / presynaptic membrane / G alpha (i) signalling events / chemical synaptic transmission / postsynaptic membrane / receptor complex / neuron projection / G protein-coupled receptor signaling pathway / protein heterodimerization activity / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zheng, S. / Kruse, A.C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for KCTD-mediated rapid desensitization of GABABsignalling. Authors: Zheng, S. / Abreu, N. / Levitz, J. / Kruse, A.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 220.1 KB | Display | ![]() |
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PDB format | ![]() | 177.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6m8sC ![]() 5a15S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12220.125 Da / Num. of mol.: 10 / Fragment: UNP residues 23-124 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q68DU8 #2: Protein/peptide | Mass: 4520.067 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: O75899 #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM magnesium chloride, 100 mM Tris-HCl, pH 7.5, 12% w/v PEG8000 |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2017 |
Radiation | Monochromator: double crystal cryo-cooled 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: 3.2→50 Å / Num. obs: 22162 / % possible obs: 99.2 % / Redundancy: 3.3 % / CC1/2: 0.926 / Rmerge(I) obs: 0.332 / Rpim(I) all: 0.208 / Rrim(I) all: 0.394 / Net I/σ(I): 3.4 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.997 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1073 / CC1/2: 0.561 / Rpim(I) all: 0.703 / Rrim(I) all: 1.226 / % possible all: 96.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5A15 Resolution: 3.2→38.639 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→38.639 Å
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Refine LS restraints |
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LS refinement shell |
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