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- PDB-5h8f: Structure of the apo human GluN1/GluN2A LBD -

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Basic information

Entry
Database: PDB / ID: 5h8f
TitleStructure of the apo human GluN1/GluN2A LBD
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsTRANSPORT PROTEIN / GluN1 / GluN2A / NMDA / receptor
Function / homologyReceptor, ligand binding region / RAF/MAP kinase cascade / Periplasmic binding protein-like I / Receptor family ligand binding region / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / N-methyl D-aspartate receptor 2B3 C-terminus / Ligated ion channel L-glutamate- and glycine-binding site / EPHB-mediated forward signaling ...Receptor, ligand binding region / RAF/MAP kinase cascade / Periplasmic binding protein-like I / Receptor family ligand binding region / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / N-methyl D-aspartate receptor 2B3 C-terminus / Ligated ion channel L-glutamate- and glycine-binding site / EPHB-mediated forward signaling / Ras activation upon Ca2+ influx through NMDA receptor / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Unblocking of NMDA receptors, glutamate binding and activation / Neurexins and neuroligins / MECP2 regulates neuronal receptors and channels / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / Long-term potentiation / Synaptic adhesion-like molecules / Negative regulation of NMDA receptor-mediated neuronal transmission / Ligand-gated ion channel / propylene metabolic process / response to glycine / pons maturation / protein localization to postsynaptic membrane / directional locomotion / excitatory chemical synaptic transmission / conditioned taste aversion / olfactory learning / regulation of respiratory gaseous exchange / serotonin metabolic process / startle response / glutamate receptor signaling pathway / regulation of synapse assembly / sleep / glutamate-gated calcium ion channel activity / neurotransmitter binding / calcium ion transmembrane import into cytosol / neurogenesis / cation transport / respiratory gaseous exchange / calcium ion homeostasis / activation of cysteine-type endopeptidase activity / glycine binding / NMDA glutamate receptor activity / glutamate binding / NMDA selective glutamate receptor complex / dopamine metabolic process / regulation of dendrite morphogenesis / synaptic membrane / suckling behavior / positive regulation of cysteine-type endopeptidase activity / social behavior / positive regulation of reactive oxygen species biosynthetic process / male mating behavior / regulation of axonogenesis / synaptic transmission, glutamatergic / postsynaptic density membrane / response to morphine / positive regulation of calcium ion transport into cytosol / excitatory synapse / long-term memory / excitatory postsynaptic potential / synaptic cleft / positive regulation of excitatory postsynaptic potential / regulation of membrane potential / prepulse inhibition / adult locomotory behavior / sensory perception of pain / integral component of postsynaptic density membrane / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / response to amphetamine / regulation of sensory perception of pain / visual learning / regulation of synaptic plasticity / long-term synaptic potentiation / ionotropic glutamate receptor signaling pathway / cerebral cortex development / regulation of long-term neuronal synaptic plasticity / memory / positive regulation of long-term synaptic potentiation / presynaptic membrane / terminal bouton / ephrin receptor signaling pathway / negative regulation of protein catabolic process / protein heterotetramerization / postsynaptic membrane / synaptic vesicle / response to wounding / learning or memory / brain development / Ras guanyl-nucleotide exchange factor activity / chemical synaptic transmission / amyloid-beta binding / calmodulin binding / response to ethanol / negative regulation of neuron apoptotic process / dendritic spine / MAPK cascade / postsynaptic density
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 1.81 Å resolution
AuthorsWallweber, H.J.A. / Lupardus, P.J.
CitationJournal: Neuron / Year: 2016
Title: Positive Allosteric Modulators of GluN2A-Containing NMDARs with Distinct Modes of Action and Impacts on Circuit Function.
Authors: Hackos, D.H. / Lupardus, P.J. / Grand, T. / Chen, Y. / Wang, T.M. / Reynen, P. / Gustafson, A. / Wallweber, H.J. / Volgraf, M. / Sellers, B.D. / Schwarz, J.B. / Paoletti, P. / Sheng, M. / Zhou, Q. / Hanson, J.E.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 23, 2015 / Release: Feb 24, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 24, 2016Structure modelrepositoryInitial release
1.1Apr 18, 2018Structure modelData collection / Database references / Derived calculationscitation / citation_author / pdbx_struct_oper_list_citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation

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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)66,06710
Polyers65,2932
Non-polymers7758
Water7,422412
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3930
ΔGint (kcal/M)-9
Surface area (Å2)24350
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)54.268, 89.193, 124.739
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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

#1: Protein/peptide 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: UNP residues 401-539, GT linker, UNP residues 661-802
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN2A, NMDAR2A / Production host: Escherichia coli (E. coli) / References: UniProt: Q12879
#2: Protein/peptide 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: UNP residues 394-544, GT linker, UNP residues 663-800
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN1, NMDAR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05586

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Non-polymers , 4 types, 420 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Formula: C3H8O3 / Glycerol
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Mass: 147.129 Da / Num. of mol.: 1 / Formula: C5H9NO4 / Glutamic acid
#5: Chemical ChemComp-GLY / GLYCINE


Mass: 75.067 Da / Num. of mol.: 1 / Formula: C2H5NO2 / Glycine
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 / Density percent sol: 46.8 %
Crystal growTemp: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate)

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Collection date: Nov 19, 2010
RadiationMonochromator: diamond(111) / Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 25.28 Å2 / D resolution high: 1.81 Å / D resolution low: 50 Å / Number obs: 55343 / Rmerge I obs: 0.03 / NetI over sigmaI: 21.9 / Redundancy: 4.9 % / Percent possible obs: 99.2
Reflection shellRmerge I obs: 0.577 / Highest resolution: 1.81 Å / Lowest resolution: 1.87 Å / MeanI over sigI obs: 2.9 / Redundancy: 4.8 % / Percent possible all: 98.4

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A5T
Correlation coeff Fo to Fc: 0.9553 / Correlation coeff Fo to Fc free: 0.9466 / Overall SU R Cruickshank DPI: 0.118 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall SU R Blow DPI: 0.123 / Overall SU R free Blow DPI: 0.114 / Overall SU R free Cruickshank DPI: 0.111
Displacement parametersB iso mean: 29.11 Å2 / Aniso B11: 2.9235 Å2 / Aniso B12: 0 Å2 / Aniso B13: 0 Å2 / Aniso B22: -3.6478 Å2 / Aniso B23: 0 Å2 / Aniso B33: 0.7244 Å2
Least-squares processR factor R free: 0.2069 / R factor R work: 0.1764 / R factor obs: 0.178 / Highest resolution: 1.81 Å / Lowest resolution: 29.44 Å / Number reflection R free: 2796 / Number reflection obs: 55343 / Percent reflection R free: 5.05 / Percent reflection obs: 98.89
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refine hist #1Highest resolution: 1.81 Å / Lowest resolution: 29.44 Å
Number of atoms included #1Protein: 4429 / Nucleic acid: 0 / Ligand: 51 / Solvent: 412 / Total: 4892
Refine LS restraints
Refine IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0104563HARMONIC2.00
X-RAY DIFFRACTIONt_angle_deg1.016172HARMONIC2.00
X-RAY DIFFRACTIONt_dihedral_angle_d1600SINUSOIDAL2.00
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes109HARMONIC2.00
X-RAY DIFFRACTIONt_gen_planes661HARMONIC5.00
X-RAY DIFFRACTIONt_it4563HARMONIC20.00
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion15.06
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion596SEMIHARMONIC5.00
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_contact5630SEMIHARMONIC4.00
Refine LS shellHighest resolution: 1.81 Å / R factor R free: 0.2813 / R factor R work: 0.215 / R factor all: 0.2184 / Lowest resolution: 1.86 Å / Number reflection R free: 196 / Number reflection R work: 3595 / Number reflection all: 3791 / Total number of bins used: 20 / Percent reflection R free: 5.17 / Percent reflection obs: 98.89

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