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Yorodumi- PDB-1lbc: Crystal structure of GluR2 ligand binding core (S1S2J-N775S) in c... -
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-Basic information
Entry | Database: PDB / ID: 1lbc | ||||||
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Title | Crystal structure of GluR2 ligand binding core (S1S2J-N775S) in complex with cyclothiazide (CTZ) as well as glutamate at 1.8 A resolution | ||||||
Components | Glutamine Receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / AMPA receptor / GluR2 / S1S2 / ligand binding core / point mutation / N775S / cyclothiazide / CTZ / agonist | ||||||
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 / rigid body refinement / Resolution: 1.8 Å | ||||||
Authors | Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E. | ||||||
Citation | Journal: Nature / Year: 2002 Title: Mechanism of glutamate receptor desensitization. Authors: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E. | ||||||
History |
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Remark 999 | Sequence The native GLUR-2 is a membrane protein. The protein crystallized by the author is the ...Sequence The native GLUR-2 is a membrane protein. The protein crystallized by the author is the extracellular ligand binding domain of GLUR-2. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker. The sequence, as a result, matches discontinuously with the reference database. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lbc.cif.gz | 165.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lbc.ent.gz | 130.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lbc_validation.pdf.gz | 613.2 KB | Display | wwPDB validaton report |
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Full document | 1lbc_full_validation.pdf.gz | 630.1 KB | Display | |
Data in XML | 1lbc_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 1lbc_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/1lbc ftp://data.pdbj.org/pub/pdb/validation_reports/lb/1lbc | HTTPS FTP |
-Related structure data
Related structure data | 1lb8C 1lb9C 1lbbC 1ftjS 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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Unit cell |
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-Components
#1: Protein | Mass: 29194.658 Da / Num. of mol.: 3 / Fragment: ligand binding core / Mutation: N775S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GluR-2 / Plasmid: pETGQ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19491*PLUS #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.52 Å3/Da / Density % sol: 51.09 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: pEG 8000 Zn(oAc)2, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9196 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9196 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 81971 / Num. obs: 81971 / % possible obs: 99.6 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 98.8 |
Reflection | *PLUS Lowest resolution: 30 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 98.8 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 4 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body refinement Starting model: PDB entry 1FTJ Resolution: 1.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor obs: 0.222 / Rfactor Rfree: 0.243 / Rfactor Rwork: 0.222 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |