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- PDB-6m8s: Crystal structure of the KCTD12 H1 domain in complex with Gbeta1g... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m8s | ||||||
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Title | Crystal structure of the KCTD12 H1 domain in complex with Gbeta1gamma2 subunits | ||||||
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![]() | SIGNALING PROTEIN / beta-propeller / homopentamer / GABAB desensitization | ||||||
Function / homology | ![]() cell projection / Olfactory Signaling Pathway / Activation of the phototransduction cascade / protein homooligomerization / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels ...cell projection / Olfactory Signaling Pathway / Activation of the phototransduction cascade / protein homooligomerization / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / postsynaptic membrane / cell population proliferation / Ras protein signal transduction / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / protein-containing complex binding / signal transduction / RNA binding / extracellular exosome / identical protein binding / membrane / plasma membrane / cytoplasm / cytosol 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 | ![]() | 472.2 KB | Display | ![]() |
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PDB format | ![]() | 386.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 548.2 KB | Display | ![]() |
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Full document | ![]() | 583.5 KB | Display | |
Data in XML | ![]() | 82.8 KB | Display | |
Data in CIF | ![]() | 111.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m8rC ![]() 1omwS 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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Unit cell |
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Components
#1: Protein | Mass: 38534.062 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 7845.078 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 14598.107 Da / Num. of mol.: 5 / Fragment: UNP residues 200-325 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q96CX2 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium chloride, 0.1 M sodium cacodylate, 8% 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: Apr 19, 2018 |
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: 3.71→50 Å / Num. obs: 29623 / % possible obs: 99 % / Redundancy: 3.9 % / Net I/σ(I): 3.56 |
Reflection shell | Resolution: 3.71→3.8 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.059 / Mean I/σ(I) obs: 1.09 / Num. unique obs: 2129 / CC1/2: 0.52 / Rrim(I) all: 1.213 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1OMW Resolution: 3.71→48.406 Å / SU ML: 0.61 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.35 / 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: 3.71→48.406 Å
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Refine LS restraints |
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LS refinement shell |
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