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- PDB-1nnp: X-ray structure of the GluR2 ligand-binding core (S1S2J) in compl... -
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Basic information
Entry | Database: PDB / ID: 1nnp | ||||||
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Title | X-ray structure of the GluR2 ligand-binding core (S1S2J) in complex with (S)-ATPA at 1.9 A resolution. Crystallization without zinc ions. | ||||||
![]() | Glutamate receptor 2 | ||||||
![]() | MEMBRANE PROTEIN / Ionotropic glutamate receptor GluR2 / ligand-binding core / agonist complex. | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lunn, M.L. / Hogner, A. / Stensbol, T.B. / Gouaux, E. / Egebjerg, J. / Kastrup, J.S. | ||||||
![]() | ![]() Title: Three-Dimensional Structure of the Ligand-Binding Core of GluR2 in Complex with the Agonist (S)-ATPA: Implications for Receptor Subunit Selectivity. Authors: Lunn, M.L. / Hogner, A. / Stensbol, T.B. / Gouaux, E. / Egebjerg, J. / Kastrup, J.S. #1: ![]() Title: Structural basis for AMPA receptor activation and ligand selectivity: Crystal structures of five agonist complexes with the GluR2 ligand binding core. Authors: Hogner, A. / Kastrup, J.S. / Jin, R. / Liljefors, T. / Mayer, M.L. / Egebjerg, J. / Larsen, I. / Gouaux, E. #2: ![]() Title: Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: Crystal structures of the GluR2 ligand binding core. Authors: Armstrong, N. / Gouaux, E. #3: ![]() Title: Mechanism of glutamate receptor desensitization. Authors: Sun, Y. / Olson, R. / Horning, M. / Armstrong, N. / Mayer, M. / Gouaux, E. #4: ![]() Title: Probing the ligand binding domain of the GluR2 receptor by proteolysis and deletion mutagenesis defines domain boundaries and yields a crystallizable construct. Authors: Chen, G.Q. / Sun, R. / Jin, R. / Gouaux, E. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). NOTE THAT COORDINATES FOR ONE DIMER OF A COMPLETE TETRAMERIC MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN IN REMARK 350. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. | ||||||
Remark 999 | SEQUENCE Native GluR2 is a membrane protein. The protein crystallized is the extracellular ligand- ...SEQUENCE Native GluR2 is a membrane protein. The protein crystallized is the extracellular ligand-binding core of GluR2. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker (residues 115-116). Therefore, the sequence matches discontinuously with the reference database (413-527, 653-796). The two first residues of the sequence (Gly-2, Ala-1) are cloning artifacts and were not located in the electron density map. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 133.1 KB | Display | ![]() |
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PDB format | ![]() | 102.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 405.2 KB | Display | ![]() |
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Full document | ![]() | 412.5 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a tetramer composed of dimers-of-dimers. Only the dimer is observed in the crystal. The dimer may be generated by applying the following to chain B: TRANSFORM FRACTIONAL - 1.00000 0.00000 0.00000 - 0.00000 -1.00000 0.00000 - 0.00000 0.00000 -1.00000 - -0.50000 0.50000 1.00000 |
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Components
#1: Protein | Mass: 29221.682 Da / Num. of mol.: 2 / Fragment: GluR2-flop ligand-binding core (S1S2J) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: ammonium sulfate, PEG8000, sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 279K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 6 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 25, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.076 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 40611 / Num. obs: 40611 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3546 / % possible all: 81.6 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS % possible obs: 81.6 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: GluR2:(S)-ATPA complex (zinc form). Resolution: 1.9→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 2164674.72 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The first three N-terminal residues and the last two C-terminal residues were not located in the electron density map.
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Solvent computation | Bsol: 48.6949 Å2 / ksol: 0.360816 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file | Serial no: 1 / Param file: protein_rep.param / Topol file: protein.top | ||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 4.6 % / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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