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- PDB-3oel: Crystal structure of GluN2D ligand-binding core in complex with D... -

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Basic information

Entry
Database: PDB / ID: 3oel
TitleCrystal structure of GluN2D ligand-binding core in complex with D-glutamate
ComponentsGlutamate [NMDA] receptor subunit epsilon-4
KeywordsTRANSPORT PROTEIN / Ion channel / D-glutamate / disulfide bonds
Function / homology
Function and homology information


regulation of sensory perception of pain / Assembly and cell surface presentation of NMDA receptors / cellular response to L-glutamate / regulation of monoatomic cation transmembrane transport / voltage-gated monoatomic cation channel activity / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / RAF/MAP kinase cascade / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol ...regulation of sensory perception of pain / Assembly and cell surface presentation of NMDA receptors / cellular response to L-glutamate / regulation of monoatomic cation transmembrane transport / voltage-gated monoatomic cation channel activity / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / RAF/MAP kinase cascade / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / glutamate binding / startle response / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / ionotropic glutamate receptor complex / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation channel activity / glutamate-gated receptor activity / glutamate-gated calcium ion 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 / positive regulation of synaptic transmission, glutamatergic / adult locomotory behavior / excitatory postsynaptic potential / synaptic transmission, glutamatergic / long-term synaptic potentiation / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / postsynaptic membrane / glutamatergic synapse / synapse / endoplasmic reticulum membrane / plasma membrane
Similarity search - Function
Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region ...Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-GLUTAMIC ACID / Glutamate receptor ionotropic, NMDA 2D
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSimorowski, N. / Furukawa, H.
CitationJournal: Nat Commun / Year: 2011
Title: Ligand-specific deactivation time course of GluN1/GluN2D NMDA receptors.
Authors: Vance, K.M. / Simorowski, N. / Traynelis, S.F. / Furukawa, H.
History
DepositionAug 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate [NMDA] receptor subunit epsilon-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1892
Polymers32,0421
Non-polymers1471
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.731, 114.195, 95.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glutamate [NMDA] receptor subunit epsilon-4 / N-methyl D-aspartate receptor subtype 2D / NMDAR2D / NR2D


Mass: 32041.617 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 424-564, 686-827
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GluN2D, Grin2d / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB(DE3) / References: UniProt: Q62645
#2: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.5 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2008
RadiationMonochromator: yale / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 25949 / % possible obs: 99.8 %

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.55 Å / SU ML: 1.61 / σ(F): 0.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 1275 5.07 %random
Rwork0.193 ---
obs0.1945 25364 96.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.111 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.5138 Å20 Å2-0 Å2
2---0.0161 Å2-0 Å2
3----4.4978 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2060 0 10 239 2309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052113
X-RAY DIFFRACTIONf_angle_d0.9782849
X-RAY DIFFRACTIONf_dihedral_angle_d17.52777
X-RAY DIFFRACTIONf_chiral_restr0.067316
X-RAY DIFFRACTIONf_plane_restr0.004368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9760.30431350.21122422X-RAY DIFFRACTION90
1.976-2.06590.24431400.19142550X-RAY DIFFRACTION94
2.0659-2.17460.20131200.18062602X-RAY DIFFRACTION96
2.1746-2.31070.21131240.17742611X-RAY DIFFRACTION95
2.3107-2.48880.23131480.18952646X-RAY DIFFRACTION97
2.4888-2.73860.23481410.20162673X-RAY DIFFRACTION98
2.7386-3.13350.22711530.2052716X-RAY DIFFRACTION99
3.1335-3.94270.21221530.18292772X-RAY DIFFRACTION100
3.9427-19.61550.20641610.19232870X-RAY DIFFRACTION100

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