+Open data
-Basic information
Entry | Database: PDB / ID: 3m3f | ||||||
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Title | PEPA bound to the ligand binding domain of GluA3 (flop form) | ||||||
Components | Glutamate receptor 3 | ||||||
Keywords | TRANSPORT PROTEIN / glutamate receptor / GluA3 / GluR3 / AMPA receptor / neurotransmitter receptor / S1S2 | ||||||
Function / homology | Function and homology information chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / glutamate-gated calcium ion channel activity / protein heterotetramerization / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion ...chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / glutamate-gated calcium ion channel activity / protein heterotetramerization / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane potential / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / monoatomic ion transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendritic shaft / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / long-term synaptic potentiation / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / amyloid-beta binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / protein homotetramerization / dendritic spine / postsynaptic density / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å | ||||||
Authors | Ahmed, A.H. / Ptak, C.P. / Oswald, R.E. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Molecular mechanism of flop selectivity and subsite recognition for an AMPA receptor allosteric modulator: structures of GluA2 and GluA3 in complexes with PEPA. Authors: Ahmed, A.H. / Ptak, C.P. / Oswald, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3m3f.cif.gz | 69.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3m3f.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 3m3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3m3f_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3m3f_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3m3f_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 3m3f_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/3m3f ftp://data.pdbj.org/pub/pdb/validation_reports/m3/3m3f | HTTPS FTP |
-Related structure data
Related structure data | 3m3kC 3m3lC 3dlnS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 28970.402 Da / Num. of mol.: 1 / Fragment: UNP residues 417-530, 658-799 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria3, Glur3 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P19492 | ||
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#2: Chemical | ChemComp-GLU / | ||
#3: Chemical | ChemComp-P99 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 14-15% PEG 8K, 0.1 M sodium cacodylate, 0.1-0.15 M zinc acetate, 0.25 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 6, 2009 |
Radiation | Monochromator: Rh coated Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.497→50 Å / Num. obs: 9141 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 19.222 |
Reflection shell | Resolution: 2.497→2.54 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.455 / Num. unique all: 432 / Rsym value: 0.455 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Starting model: PDB entry 3DLN Resolution: 2.5→36.489 Å / SU ML: 0.41 / σ(F): 0.75 / Phase error: 28.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.075 Å2 / ksol: 0.328 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→36.489 Å
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Refine LS restraints |
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LS refinement shell |
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