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Yorodumi- PDB-6yk5: Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yk5 | ||||||
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Title | Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the compound (S)-1-(2'-Amino-2'-carboxyethyl)-5,7-dihydrofuro[3,4-d]- pyrimidine-2,4(1H,3H)-dione at resolution 1.15A | ||||||
Components | Glutamate receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / GLUA2O LIGAND-BINDING DOMAIN / BICYCLIC PYRIMIDINEDIONE ANALOGUE | ||||||
Function / homology | Function and homology information spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / terminal bouton / receptor internalization / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | ||||||
Authors | Frydenvang, K. / Kastrup, J.S. | ||||||
Citation | Journal: Acs Chem Neurosci / Year: 2020 Title: Ionotropic Glutamate Receptor GluA2 in Complex with Bicyclic Pyrimidinedione-Based Compounds: When Small Compound Modifications Have Distinct Effects on Binding Interactions. Authors: Frydenvang, K. / Pickering, D.S. / Kshirsagar, G.U. / Chemi, G. / Gemma, S. / Sprogoe, D. / Kærn, A.M. / Brogi, S. / Campiani, G. / Butini, S. / Kastrup, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yk5.cif.gz | 146 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yk5.ent.gz | 112.9 KB | Display | PDB format |
PDBx/mmJSON format | 6yk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yk5_validation.pdf.gz | 772.3 KB | Display | wwPDB validaton report |
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Full document | 6yk5_full_validation.pdf.gz | 772.3 KB | Display | |
Data in XML | 6yk5_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 6yk5_validation.cif.gz | 26.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/6yk5 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/6yk5 | HTTPS FTP |
-Related structure data
Related structure data | 6yk2C 6yk3C 6yk4C 6yk6C 1syhS 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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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 29278.732 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUA2O. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUE 118-119). THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUA2O. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUE 118-119). THE SEQUENCE MATCHES DISCONTINOUSLY WITH THE REFERENCE DATABASE (UNP RESIDUES 413-527 AND 653-797, NUMBERING WITH SIGNAL PEPTIDE OF 21 AMINO ACIDS). THE TWO FIRST RESIDUES (GLY, ALA) ARE CLONING REMNANTS. Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Plasmid: PET-22B(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): ORIGAMI B (DE3) / References: UniProt: P19491 |
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-Non-polymers , 6 types, 459 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-LI / | #5: Chemical | ChemComp-PVK / ( | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.36 Å3/Da / Density % sol: 47.83 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG4000, lithium sulfate, acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 14, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.15→28.212 Å / Num. all: 97655 / Num. obs: 97655 / % possible obs: 98.6 % / Redundancy: 4.6 % / Biso Wilson estimate: 7.97 Å2 / Rpim(I) all: 0.032 / Rrim(I) all: 0.069 / Rsym value: 0.061 / Net I/av σ(I): 7.6 / Net I/σ(I): 14.2 / Num. measured all: 450981 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SYH Resolution: 1.15→26.778 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 9.7
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.22 Å2 / Biso mean: 12.6496 Å2 / Biso min: 4.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.15→26.778 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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