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- PDB-5h8n: Structure of the human GluN1/GluN2A LBD in complex with NAM -

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Basic information

Entry
Database: PDB / ID: 5h8n
TitleStructure of the human GluN1/GluN2A LBD in complex with NAM
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsTRANSPORT PROTEIN / GluN1 / GluN2A / NMDA / receptor
Function / homology
Function and homology information


glycine-gated cation channel activity / excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / response to glycine / propylene metabolic process / sleep / Assembly and cell surface presentation of NMDA receptors ...glycine-gated cation channel activity / excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / response to glycine / propylene metabolic process / sleep / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / Neurexins and neuroligins / glutamate binding / ligand-gated sodium channel activity / neurotransmitter receptor complex / glutamate receptor signaling pathway / calcium ion transmembrane import into cytosol / protein heterotetramerization / glycine binding / startle response / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / dopamine metabolic process / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of calcium ion transport into cytosol / Long-term potentiation / excitatory synapse / monoatomic cation transport / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / positive regulation of excitatory postsynaptic potential / synaptic cleft / positive regulation of synaptic transmission, glutamatergic / calcium ion homeostasis / MECP2 regulates neuronal receptors and channels / glutamate-gated calcium ion channel activity / neurogenesis / EPHB-mediated forward signaling / sensory perception of pain / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / cytoplasmic vesicle membrane / synaptic membrane / response to amphetamine / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / protein catabolic process / postsynaptic density membrane / brain development / visual learning / negative regulation of protein catabolic process / regulation of synaptic plasticity / calcium ion transmembrane transport / response to wounding / memory / long-term synaptic potentiation / terminal bouton / synaptic vesicle / signaling receptor activity / amyloid-beta binding / presynaptic membrane / RAF/MAP kinase cascade / response to ethanol / chemical synaptic transmission / dendritic spine / postsynaptic membrane / learning or memory / calmodulin binding / neuron projection / postsynaptic density / positive regulation of apoptotic process / response to xenobiotic stimulus / dendrite / calcium ion binding / synapse / endoplasmic reticulum membrane / protein-containing complex binding / glutamatergic synapse / 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 / : / : / 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 / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / 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
Chem-5YD / 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: 2.5 Å
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.
History
DepositionDec 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _citation.journal_id_ISSN ..._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
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,9546
Polymers65,2932
Non-polymers6624
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-14 kcal/mol
Surface area24600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.655, 89.791, 124.695
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,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 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,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 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, 142 molecules

#3: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-5YD / 4-[[(4-fluorophenyl)sulfonylamino]methyl]-~{N}-(pyridin-3-ylmethyl)benzamide


Mass: 399.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18FN3O3S
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 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 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 29, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→37.72 Å / Num. obs: 21755 / % possible obs: 99.4 % / Redundancy: 6 % / Biso Wilson estimate: 40.99 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 4.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A5T

2a5t


Resolution: 2.5→27.02 Å / Cor.coef. Fo:Fc: 0.9317 / Cor.coef. Fo:Fc free: 0.8965 / SU R Cruickshank DPI: 0.505 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.555 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.269
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 1103 5.07 %RANDOM
Rwork0.1791 ---
obs0.182 21755 99.36 %-
Displacement parametersBiso mean: 30.77 Å2
Baniso -1Baniso -2Baniso -3
1-4.6617 Å20 Å20 Å2
2---2.0586 Å20 Å2
3----2.6031 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 2.5→27.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4381 0 44 138 4563
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014507HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.116100HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1553SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes106HARMONIC2
X-RAY DIFFRACTIONt_gen_planes651HARMONIC5
X-RAY DIFFRACTIONt_it4507HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion18.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion589SEMIHARMONIC5
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_contact5069SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.62 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.29 140 4.9 %
Rwork0.2162 2720 -
all0.2197 2860 -
obs--99.36 %

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