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- PDB-4tk4: GephE in complex with a GABA receptor alpha3 subunit derived doub... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4tk4 | ||||||
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Title | GephE in complex with a GABA receptor alpha3 subunit derived double mutant peptide in space group P61 | ||||||
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![]() | BIOSYNTHETIC PROTEIN / Structural Protein / Scaffolding protein / Neurotransmitter receptor anchoring / Molybdenum co factor bio synthesis | ||||||
Function / homology | ![]() GABA receptor activation / Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / gamma-aminobutyric acid receptor clustering / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity ...GABA receptor activation / Molybdenum cofactor biosynthesis / glycine receptor clustering / molybdopterin cofactor biosynthetic process / establishment of synaptic specificity at neuromuscular junction / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / gamma-aminobutyric acid receptor clustering / molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / nitrate reductase activity / postsynaptic specialization / inhibitory synapse / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / Mo-molybdopterin cofactor biosynthetic process / glycinergic synapse / postsynaptic neurotransmitter receptor diffusion trapping / synaptic transmission, GABAergic / response to metal ion / gamma-aminobutyric acid signaling pathway / molybdopterin cofactor binding / postsynaptic specialization membrane / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic specialization, intracellular component / chloride channel complex / transmembrane transporter complex / GABA-ergic synapse / regulation of postsynaptic membrane potential / protein targeting / presynaptic active zone membrane / chloride transmembrane transport / synapse assembly / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / tubulin binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / establishment of protein localization / cytoplasmic side of plasma membrane / protein-macromolecule adaptor activity / chemical synaptic transmission / postsynaptic membrane / postsynapse / molecular adaptor activity / postsynaptic density / cytoskeleton / neuron projection / signaling receptor binding / neuronal cell body / synapse / dendrite / ATP binding / identical protein binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kasaragod, V.B. / Maric, H.M. / Schindelin, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of the alternative recruitment of GABAA versus glycine receptors through gephyrin. Authors: Maric, H.M. / Kasaragod, V.B. / Hausrat, T.J. / Kneussel, M. / Tretter, V. / Strmgaard, K. / Schindelin, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 338.9 KB | Display | ![]() |
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PDB format | ![]() | 279.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4tk1C ![]() 4tk2C ![]() 4tk3C ![]() 2fu3S 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: 45652.395 Da / Num. of mol.: 2 / Fragment: domain E (UNP residues 344-762) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q03555, molybdopterin adenylyltransferase, molybdopterin molybdotransferase #2: Protein/peptide | Mass: 1223.418 Da / Num. of mol.: 2 / Fragment: UNP residues 396-406 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.05 Å3/Da / Density % sol: 75.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.15 M Calcium acetate, 0.1 M sodium cacodylate pH 6.0, 6-10 % Isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→67.89 Å / Num. obs: 21728 / % possible obs: 100 % / Redundancy: 5.6 % / Rsym value: 0.15 / Net I/σ(I): 7.6 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: 2FU3 Resolution: 3.601→67.88 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 22.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.601→67.88 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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