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- PDB-9mum: Crystal structure of GluN1/GluN2A ligand-binding domain in comple... -

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Basic information

Entry
Database: PDB / ID: 9mum
TitleCrystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 11, Glycine and Glutamate
Components(Glutamate receptor ionotropic, NMDA ...) x 2
KeywordsMEMBRANE PROTEIN / NMDARS / LBD / ION CHANNELS / METAL TRANSPORT / NEGATIVE MODULATOR
Function / homology
Function and homology information


glycine-gated cation channel activity / excitatory chemical synaptic transmission / directional locomotion / serotonin metabolic process / Synaptic adhesion-like molecules / protein localization to postsynaptic membrane / response to glycine / propylene metabolic process / sleep / regulation of monoatomic cation transmembrane transport ...glycine-gated cation channel activity / excitatory chemical synaptic transmission / directional locomotion / serotonin metabolic process / Synaptic adhesion-like molecules / protein localization to postsynaptic membrane / response to glycine / propylene metabolic process / sleep / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / Neurexins and neuroligins / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / calcium ion transmembrane import into cytosol / glutamate receptor signaling pathway / glutamate binding / protein heterotetramerization / glycine binding / positive regulation of reactive oxygen species biosynthetic process / positive regulation of calcium ion transport into cytosol / Negative regulation of NMDA receptor-mediated neuronal transmission / startle response / dopamine metabolic process / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / Long-term potentiation / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / monoatomic ion channel complex / synaptic cleft / calcium ion homeostasis / MECP2 regulates neuronal receptors and channels / glutamate-gated calcium ion channel activity / neurogenesis / sensory perception of pain / EPHB-mediated forward signaling / sodium ion transmembrane transport / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / ionotropic glutamate receptor signaling pathway / cytoplasmic vesicle membrane / positive regulation of synaptic transmission, glutamatergic / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / synaptic membrane / protein catabolic process / postsynaptic density membrane / terminal bouton / brain development / visual learning / negative regulation of protein catabolic process / calcium ion transmembrane transport / regulation of synaptic plasticity / memory / response to wounding / long-term synaptic potentiation / synaptic vesicle / signaling receptor activity / amyloid-beta binding / presynaptic membrane / RAF/MAP kinase cascade / chemical synaptic transmission / dendritic spine / response to ethanol / postsynaptic membrane / learning or memory / calmodulin binding / neuron projection / postsynaptic density / positive regulation of apoptotic process / response to xenobiotic stimulus / synapse / dendrite / calcium ion binding / 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 I
Similarity search - Domain/homology
: / 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: 1.97 Å
AuthorsShaffer, P.L. / Duda, D.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Design, Synthesis, and Characterization of GluN2A Negative Allosteric Modulators Suitable for In Vivo Exploration.
Authors: Bischoff, F.P. / Van Brandt, S. / Viellevoye, M. / De Cleyn, M. / Surkyn, M. / Carbajo, R.J. / Dominguez Blanco, M. / Wroblowski, B. / Karpowich, N.K. / Steele, R.A. / Schalk-Hihi, C. / ...Authors: Bischoff, F.P. / Van Brandt, S. / Viellevoye, M. / De Cleyn, M. / Surkyn, M. / Carbajo, R.J. / Dominguez Blanco, M. / Wroblowski, B. / Karpowich, N.K. / Steele, R.A. / Schalk-Hihi, C. / Miller, R. / Duda, D. / Shaffer, P. / Ballentine, S. / Simavorian, S. / Lord, B. / Neff, R.A. / Bonaventure, P. / Gijsen, H.J.M.
History
DepositionJan 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,3695
Polymers68,7152
Non-polymers6543
Water4,396244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-6 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.500, 90.000, 124.940
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 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1 / hNR1


Mass: 35163.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN1, NMDAR1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2 (DE3) / References: UniProt: Q05586
#2: Protein Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / ...GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NMDAR2A / NR2A / hNR2A


Mass: 33551.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN2A, NMDAR2A / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2 (DE3) / References: UniProt: Q12879

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Non-polymers , 4 types, 247 molecules

#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C5H9NO4
#5: Chemical ChemComp-A1BRB / 5-[2-(3-chlorophenyl)-2,2-difluoroethoxy]-N-[1-(pyrazin-2-yl)cyclopropyl]pyrazine-2-carboxamide


Mass: 431.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H16ClF2N5O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Hepes pH 7.0, 0.2M ammonium acetate, 20% PEG-3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→37.8 Å / Num. obs: 40128 / % possible obs: 90.9 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 18.9
Reflection shellResolution: 1.97→2.01 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2182 / CC1/2: 0.735 / Rpim(I) all: 0.367 / Rrim(I) all: 0.963 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEMar 15, 2019 (BUILT 20191211)data scaling
XDSMar 15, 2019 (BUILT 20191211)data reduction
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→37.8 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 2051 5.11 %
Rwork0.1919 --
obs0.1944 40117 90.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→37.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 45 244 4583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074428
X-RAY DIFFRACTIONf_angle_d0.8425990
X-RAY DIFFRACTIONf_dihedral_angle_d5.731594
X-RAY DIFFRACTIONf_chiral_restr0.058666
X-RAY DIFFRACTIONf_plane_restr0.007773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.29631610.23972775X-RAY DIFFRACTION100
2.02-2.070.26551500.22572726X-RAY DIFFRACTION100
2.07-2.120.27311390.21642727X-RAY DIFFRACTION100
2.12-2.190.29111430.21332793X-RAY DIFFRACTION100
2.19-2.240.30881000.21462063X-RAY DIFFRACTION98
2.27-2.340.2481260.20022466X-RAY DIFFRACTION100
2.34-2.430.24861460.20032761X-RAY DIFFRACTION100
2.43-2.540.28491610.20922750X-RAY DIFFRACTION100
2.54-2.610.2847740.22461531X-RAY DIFFRACTION99
2.7-2.840.2691100.22722373X-RAY DIFFRACTION100
2.84-3.060.26131380.22872792X-RAY DIFFRACTION100
3.06-3.370.26241820.20382775X-RAY DIFFRACTION100
3.37-3.860.24361140.17971948X-RAY DIFFRACTION70
3.86-4.860.19531430.15072601X-RAY DIFFRACTION91
4.86-37.80.21111640.18062985X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -13.892 Å / Origin y: -14.6113 Å / Origin z: 25.5595 Å
111213212223313233
T0.2378 Å20.0062 Å20.0091 Å2-0.2234 Å2-0.0052 Å2--0.2797 Å2
L0.7493 °2-0.0379 °20.4291 °2-0.5303 °2-0.0412 °2--1.2597 °2
S-0.0379 Å °-0.1045 Å °0.0758 Å °0.0498 Å °0.0248 Å °-0.0915 Å °-0.081 Å °-0.0817 Å °0.0207 Å °
Refinement TLS groupSelection details: all

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