[English] 日本語
Yorodumi- PDB-5fho: Crystal structure of the GluA2 ligand-binding domain (S1S2J) in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fho | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with (S)-2-Amino-3-(5-(2-(3-chlorobenzyl)-2H-tetrazol-5-yl)-3-hydroxyisoxazol-4-yl)propanoic acid at 2.3 A resolution | ||||||
Components | Glutamate receptor 2,Glutamate receptor 2 | ||||||
Keywords | MEMBRANE PROTEIN / Ionotropic glutamate receptor GluA2 / ligand-binding domain / Signaling protein | ||||||
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: 2.3 Å | ||||||
Authors | Frydenvang, K. / Kastrup, J.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2016 Title: Tweaking Subtype Selectivity and Agonist Efficacy at (S)-2-Amino-3-(3-hydroxy-5-methyl-isoxazol-4-yl)propionic acid (AMPA) Receptors in a Small Series of BnTetAMPA Analogues. Authors: Wang, S.Y. / Larsen, Y. / Navarrete, C.V. / Jensen, A.A. / Nielsen, B. / Al-Musaed, A. / Frydenvang, K. / Kastrup, J.S. / Pickering, D.S. / Clausen, R.P. #1: Journal: J. Med. Chem. / Year: 2007 Title: A tetrazolyl-substituted subtype-selective AMPA receptor agonist. Authors: Vogensen, S.B. / Frydenvang, K. / Greenwood, J.R. / Postorino, G. / Nielsen, B. / Pickering, D.S. / Ebert, B. / Bolcho, U. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. / Johansen, T.N. / ...Authors: Vogensen, S.B. / Frydenvang, K. / Greenwood, J.R. / Postorino, G. / Nielsen, B. / Pickering, D.S. / Ebert, B. / Bolcho, U. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. / Johansen, T.N. / Clausen, R.P. / Krogsgaard-Larsen, P. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5fho.cif.gz | 401.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5fho.ent.gz | 335.3 KB | Display | PDB format |
PDBx/mmJSON format | 5fho.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fho_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5fho_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5fho_validation.xml.gz | 42.9 KB | Display | |
Data in CIF | 5fho_validation.cif.gz | 58.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fh/5fho ftp://data.pdbj.org/pub/pdb/validation_reports/fh/5fho | HTTPS FTP |
-Related structure data
Related structure data | 5fhmC 5fhnC 2p2aS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 29278.732 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Protein crystallized is the extracellular ligand-binding domain of GluA2. Transmembrane regions genetically removed and replaced with Gly-Thr linker (residues 118-119). Protein consists of ...Details: Protein crystallized is the extracellular ligand-binding domain of GluA2. Transmembrane regions genetically removed and replaced with Gly-Thr linker (residues 118-119). Protein consists of UNP residues 413-527 and 653-797, numbering with signal peptide of 21 residues. The first two residues (Gly, Ala) are cloning remnants. Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / References: UniProt: P19491 |
---|
-Non-polymers , 7 types, 459 molecules
#2: Chemical | ChemComp-5XN / ( #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-PG4 / | #8: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.42 % |
---|---|
Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG4000 ammonium sulfate acetate buffer pH 5.5 / PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→48.07 Å / Num. all: 50972 / Num. obs: 50972 / % possible obs: 100 % / Redundancy: 4.1 % / Biso Wilson estimate: 28.03 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.077 / Rsym value: 0.067 / Net I/av σ(I): 9 / Net I/σ(I): 14.6 / Num. measured all: 208313 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2P2A (molB) Resolution: 2.3→44.046 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.26 / Phase error: 20.74 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.98 Å2 / Biso mean: 36.1995 Å2 / Biso min: 13.77 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→44.046 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
|