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- PDB-2rcb: Crystal structure of the NR3B ligand binding core complex with D-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2rcb | ||||||
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Title | Crystal structure of the NR3B ligand binding core complex with D-serine at 1.62 Angstrom resolution | ||||||
![]() | Glutamate [NMDA] receptor subunit 3B | ||||||
![]() | MEMBRANE PROTEIN / Cell junction / Glycoprotein / Ion transport / Ionic channel / Magnesium / Postsynaptic cell membrane / Receptor / Synapse / Transmembrane / Transport | ||||||
Function / homology | ![]() protein insertion into membrane / glutamate receptor activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / neurotransmitter receptor activity / glycine binding / regulation of calcium ion transport / cellular response to glycine / monoatomic cation channel activity / presynaptic active zone membrane ...protein insertion into membrane / glutamate receptor activity / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / neurotransmitter receptor activity / glycine binding / regulation of calcium ion transport / cellular response to glycine / monoatomic cation channel activity / presynaptic active zone membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / calcium ion transmembrane transport / postsynaptic density membrane / modulation of chemical synaptic transmission / neuronal cell body / endoplasmic reticulum membrane / plasma membrane 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 151 AND 152 GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 561-675 OF THE PROTEIN ...RESIDUES 151 AND 152 GLY AND THR, ARE INSERTED AS A LINK REPLACING RESIDUES 561-675 OF THE PROTEIN FROM THE UNP entry Q8VHN2 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 134.3 KB | Display | ![]() |
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PDB format | ![]() | 104.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2rc7C ![]() 2rc8C ![]() 2rc9C ![]() 2rcaC ![]() 1pb7S C: citing same article ( S: Starting model for refinement |
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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. In the present structure packing is not biologically relevant |
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Components
#1: Protein | Mass: 32180.646 Da / Num. of mol.: 2 / Fragment: unp residues 413-560, 676-815 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Description: Peptides corresponding to A413-R560 and E676-K815 were coupled by a GT dipeptid e synthetic linker Gene: Grin3b / Plasmid: pET22b(+) modified / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1 M NaCitrate, 17% PEG 4000, pH 6.2, 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: Dec 10, 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: 1.62→40 Å / Num. all: 71657 / Num. obs: 71657 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.62→1.68 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3.96 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Pdb entry 1PB7 Resolution: 1.62→36.25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.529 / SU ML: 0.065 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.106 / ESU R Free: 0.105 / 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: 18.293 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→36.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.62→1.662 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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