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- PDB-2rc9: Crystal structure of the NR3A ligand binding core complex with AC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2rc9 | ||||||
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Title | Crystal structure of the NR3A ligand binding core complex with ACPC at 1.96 Angstrom resolution | ||||||
![]() | Glutamate [NMDA] receptor subunit 3A | ||||||
![]() | MEMBRANE PROTEIN / Cell junction / Glycoprotein / Ion transport / Ionic channel / Magnesium / Postsynaptic cell membrane / Receptor / Synapse / Transmembrane / Transport | ||||||
Function / homology | ![]() 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 / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / calcium channel activity / modulation of chemical synaptic transmission / 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yao, Y. / Mayer, M.L. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139.3 KB | Display | ![]() |
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PDB format | ![]() | 109.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.3 KB | Display | ![]() |
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Full document | ![]() | 449 KB | Display | |
Data in XML | ![]() | 27.2 KB | Display | |
Data in CIF | ![]() | 40.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2rc7SC ![]() 2rc8C ![]() 2rcaC ![]() 2rcbC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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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. |
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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.) ![]() ![]() 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: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 0.2 M Mg Acetate, 0.1 M NaCitrate, 14% PEG 3350, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2007 |
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: 1.96→40 Å / Num. all: 43239 / Num. obs: 43239 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.362 / Rsym value: 0.0259 / % possible all: 96.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Pdb entry 2RC7 Resolution: 1.96→19.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 6.756 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.153 / 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: 14.799 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→2.011 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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