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Yorodumi- PDB-2rc8: Crystal structure of the NR3A ligand binding core complex with D-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rc8 | ||||||
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Title | Crystal structure of the NR3A ligand binding core complex with D-serine at 1.45 Angstrom resolution | ||||||
Components | Glutamate [NMDA] receptor subunit 3A | ||||||
Keywords | MEMBRANE PROTEIN / Cell junction / Glycoprotein / Ion transport / Ionic channel / Magnesium / Postsynaptic cell membrane / Receptor / Synapse / Transmembrane / Transport | ||||||
Function / homology | Function and homology information negative regulation of dendritic spine development / Assembly and cell surface presentation of NMDA receptors / glutamate receptor activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / glycine binding / dendrite development / neuron development / prepulse inhibition / glutamate-gated receptor activity ...negative regulation of dendritic spine development / Assembly and cell surface presentation of NMDA receptors / glutamate receptor activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / glycine binding / dendrite development / neuron development / prepulse inhibition / glutamate-gated receptor activity / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / protein phosphatase 2A binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / calcium channel activity / calcium ion transport / rhythmic process / presynapse / postsynaptic membrane / response to ethanol / neuron projection / neuronal cell body / glutamatergic synapse / synapse / endoplasmic reticulum membrane / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Difference Fourier / Resolution: 1.45 Å | ||||||
Authors | Yao, Y. / Mayer, M.L. | ||||||
Citation | Journal: Embo J. / Year: 2008 Title: Molecular mechanism of ligand recognition by NR3 subtype glutamate receptors. Authors: Yao, Y. / Harrison, C.B. / Freddolino, P.L. / Schulten, K. / Mayer, M.L. #1: Journal: J.NEUROSCI. / Year: 2006 Title: Characterization of a soluble ligand binding domain of the NMDA receptor regulatory subunit NR3A Authors: Yao, Y. / Mayer, M.L. | ||||||
History |
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Remark 999 | RESIDUES 153 AND 154, GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 661-775 OF THE PROTEIN ...RESIDUES 153 AND 154, GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 661-775 OF THE PROTEIN FROM THE UNP entry Q9R1M7 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rc8.cif.gz | 142.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rc8.ent.gz | 117.7 KB | Display | PDB format |
PDBx/mmJSON format | 2rc8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rc8_validation.pdf.gz | 463.1 KB | Display | wwPDB validaton report |
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Full document | 2rc8_full_validation.pdf.gz | 470.5 KB | Display | |
Data in XML | 2rc8_validation.xml.gz | 30 KB | Display | |
Data in CIF | 2rc8_validation.cif.gz | 45.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/2rc8 ftp://data.pdbj.org/pub/pdb/validation_reports/rc/2rc8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological unit is believed to be a dimer of dimers. Molecular packing in the present structure is not biologically relevant. |
-Components
#1: Protein | Mass: 32936.301 Da / Num. of mol.: 2 / Fragment: unp residues 511-660, 776-915 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) Description: Peptides corresponding to N511-R660 and E776-K915 were coupled by a GT dipeptid e synthetic linker Gene: Grin3a / Plasmid: pET22b(+) modified / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMIB (DE3) / References: UniProt: Q9R1M7 #2: Chemical | #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: 2.21 Å3/Da / Density % sol: 44.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: 0.12 M NaSCN, 0.1M NaCitrate, 0.01 M EDTA, 11% PEG 3350, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2006 |
Radiation | Monochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→35 Å / Num. all: 100689 / Num. obs: 100689 / % possible obs: 96 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 2 % / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 2.5 / % possible all: 72.1 |
-Processing
Software |
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Refinement | Method to determine structure: Difference Fourier / Resolution: 1.45→34.84 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.941 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.952 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→34.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.49 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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