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- PDB-5kdt: Structure of the human GluN1/GluN2A LBD in complex with GNE0723 -

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Basic information

Entry
Database: PDB / ID: 5kdt
TitleStructure of the human GluN1/GluN2A LBD in complex with GNE0723
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsTRANSPORT PROTEIN / NMDA / receptor / glutamate / channel
Function / homology
Function and homology information


excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / activation of cysteine-type endopeptidase activity / glutamate-gated calcium ion channel activity ...excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / activation of cysteine-type endopeptidase activity / glutamate-gated calcium ion channel activity / glutamate receptor signaling pathway / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / glycine binding / positive regulation of calcium ion transport into cytosol / dopamine metabolic process / Negative regulation of NMDA receptor-mediated neuronal transmission / startle response / Unblocking of NMDA receptors, glutamate binding and activation / regulation of neuronal synaptic plasticity / monoatomic cation transmembrane transport / positive regulation of excitatory postsynaptic potential / Long-term potentiation / monoatomic cation transport / ligand-gated monoatomic ion channel activity / excitatory synapse / calcium ion homeostasis / synaptic cleft / MECP2 regulates neuronal receptors and channels / sensory perception of pain / response to amphetamine / EPHB-mediated forward signaling / excitatory postsynaptic potential / regulation of membrane potential / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / neurogenesis / positive regulation of synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / postsynaptic density membrane / brain development / protein catabolic process / regulation of synaptic plasticity / visual learning / cytoplasmic vesicle membrane / terminal bouton / negative regulation of protein catabolic process / memory / response to wounding / synaptic vesicle / signaling receptor activity / presynaptic membrane / amyloid-beta binding / chemical synaptic transmission / RAF/MAP kinase cascade / postsynaptic membrane / response to ethanol / dendritic spine / postsynaptic density / learning or memory / calmodulin binding / neuron projection / response to xenobiotic stimulus / positive regulation of apoptotic process / dendrite / synapse / glutamatergic synapse / calcium ion binding / protein-containing complex binding / endoplasmic reticulum membrane / cell surface / positive regulation of transcription by RNA polymerase II / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / 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
Chem-6RV / ACETATE ION / GLUTAMIC ACID / GLYCINE / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsWallweber, H.J.A. / Lupardus, P.J.
CitationJournal: J. Med. Chem. / Year: 2016
Title: Discovery of GluN2A-Selective NMDA Receptor Positive Allosteric Modulators (PAMs): Tuning Deactivation Kinetics via Structure-Based Design.
Authors: Volgraf, M. / Sellers, B.D. / Jiang, Y. / Wu, G. / Ly, C.Q. / Villemure, E. / Pastor, R.M. / Yuen, P.W. / Lu, A. / Luo, X. / Liu, M. / Zhang, S. / Sun, L. / Fu, Y. / Lupardus, P.J. / ...Authors: Volgraf, M. / Sellers, B.D. / Jiang, Y. / Wu, G. / Ly, C.Q. / Villemure, E. / Pastor, R.M. / Yuen, P.W. / Lu, A. / Luo, X. / Liu, M. / Zhang, S. / Sun, L. / Fu, Y. / Lupardus, P.J. / Wallweber, H.J. / Liederer, B.M. / Deshmukh, G. / Plise, E. / Tay, S. / Reynen, P. / Herrington, J. / Gustafson, A. / Liu, Y. / Dirksen, A. / Dietz, M.G. / Liu, Y. / Wang, T.M. / Hanson, J.E. / Hackos, D. / Scearce-Levie, K. / Schwarz, J.B.
History
DepositionJun 8, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJul 13, 2016ID: 5I2J
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 2A
B: Glutamate receptor ionotropic, NMDA 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0426
Polymers65,2932
Non-polymers7494
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-4 kcal/mol
Surface area25300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.325, 90.127, 123.185
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Glutamate receptor ionotropic, NMDA ... , 2 types, 2 molecules AB

#1: Protein Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / hNR2A


Mass: 31883.441 Da / Num. of mol.: 1
Fragment: Ligand binding domain (UNP residues 401-539, GT linker, UNP residues 661-802)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN2A, NMDAR2A / Production host: Escherichia coli (E. coli) / References: UniProt: Q12879
#2: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 33409.074 Da / Num. of mol.: 1
Fragment: Ligand binding domain (UNP residues 415-565, GT linker, UNP residues 684-821)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN1, NMDAR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05586

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Non-polymers , 5 types, 158 molecules

#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H3O2
#4: Chemical ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical ChemComp-6RV / (1~{R},2~{R})-2-[7-[[5-chloranyl-3-(trifluoromethyl)pyrazol-1-yl]methyl]-5-oxidanylidene-2-(trifluoromethyl)-[1,3]thiazolo[3,2-a]pyrimidin-3-yl]cyclopropane-1-carbonitrile


Mass: 467.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H8ClF6N5OS
#6: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H5NO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.44→90 Å / Num. obs: 23645 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 62.31 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 18.1
Reflection shellResolution: 2.44→2.57 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.802 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→72.74 Å / Cor.coef. Fo:Fc: 0.9448 / Cor.coef. Fo:Fc free: 0.9203 / SU R Cruickshank DPI: 0.425 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.458 / SU Rfree Blow DPI: 0.259 / SU Rfree Cruickshank DPI: 0.258
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 1192 5.04 %RANDOM
Rwork0.1861 ---
obs0.1888 23645 99.99 %-
Displacement parametersBiso mean: 57.44 Å2
Baniso -1Baniso -2Baniso -3
1--4.1682 Å20 Å20 Å2
2--6.8969 Å20 Å2
3----2.7287 Å2
Refine analyzeLuzzati coordinate error obs: 0.284 Å
Refinement stepCycle: LAST / Resolution: 2.44→72.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4419 0 49 154 4622
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014551HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.136163HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1575SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes107HARMONIC2
X-RAY DIFFRACTIONt_gen_planes677HARMONIC5
X-RAY DIFFRACTIONt_it4551HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion19.27
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion596SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5231SEMIHARMONIC4
LS refinement shellResolution: 2.44→2.55 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2919 134 4.68 %
Rwork0.2185 2732 -
all0.2221 2866 -
obs--99.99 %

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