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- PDB-5mfw: Crystal structure of the GluK1 ligand-binding domain in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mfw | ||||||
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Title | Crystal structure of the GluK1 ligand-binding domain in complex with kainate and BPAM-121 at 2.10 A resolution | ||||||
![]() | Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1 | ||||||
![]() | MEMBRANE PROTEIN / ionotropic glutamate receptor / GluK1 ligand-binding domain / positive allosteric modulator | ||||||
Function / homology | ![]() gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential ...gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / synaptic transmission, GABAergic / glutamate binding / adult behavior / behavioral response to pain / modulation of excitatory postsynaptic potential / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of localization in cell / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / presynaptic membrane / nervous system development / scaffold protein binding / chemical synaptic transmission / postsynaptic density / receptor complex / neuronal cell body / glutamatergic synapse / synapse / dendrite / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Larsen, A.P. / Frydenvang, K. / Kastrup, J.S. | ||||||
![]() | ![]() Title: Identification and Structure-Function Study of Positive Allosteric Modulators of Kainate Receptors. Authors: Larsen, A.P. / Fievre, S. / Frydenvang, K. / Francotte, P. / Pirotte, B. / Kastrup, J.S. / Mulle, C. #1: ![]() Title: Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate. Authors: Naur, P. / Vestergaard, B. / Skov, L.K. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 130 KB | Display | ![]() |
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PDB format | ![]() | 98.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 37.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5mfqC ![]() 5mfvC ![]() 4e0xS S: Starting model for refinement C: citing same article ( |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29108.453 Da / Num. of mol.: 2 / Fragment: UNP residues 445-559,UNP residues 682-820 Source method: isolated from a genetically manipulated source Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 545 AND 546 OF THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 545 AND 546 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (430-544, 667-805). RESIDUE 429 IS REMNANT FROM CLONING. Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 7 types, 489 molecules ![](data/chem/img/7M6.gif)
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![](data/chem/img/KAI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
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![](data/chem/img/CL.gif)
![](data/chem/img/KAI.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Chemical | ChemComp-SO4 / #6: Chemical | #7: Chemical | ChemComp-ACT / | #8: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCE DATABASE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR ...THE SEQUENCE DATABASE IS P22756-2, ISOFORM GLUR5-2. THE PROTEIN CRYSTALLIZ |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.98 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20 % PEG4000, 0.3 M lithium-sulfate, 0.1 M sodium-acetate pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→29.631 Å / Num. obs: 33935 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 22.17 Å2 / Rsym value: 0.089 / Net I/av σ(I): 6.975 / Net I/σ(I): 18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 35.66 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4E0X Resolution: 2.1→29.631 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.2 Å2 / Biso mean: 18.44 Å2 / Biso min: 2.42 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→29.631 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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