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

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Basic information

Entry
Database: PDB / ID: 9mul
TitleCrystal structure of GluN1/GluN2A ligand-binding domain in complex with Compound 1, 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 / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / sleep / response to glycine / propylene metabolic process / regulation of monoatomic cation transmembrane transport ...glycine-gated cation channel activity / excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / sleep / response to glycine / propylene metabolic process / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / Neurexins and neuroligins / ligand-gated sodium channel activity / glutamate binding / 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 / Negative regulation of NMDA receptor-mediated neuronal transmission / dopamine metabolic process / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of calcium ion transport into cytosol / Long-term potentiation / monoatomic cation transport / excitatory synapse / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / positive regulation of excitatory postsynaptic potential / synaptic cleft / 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 / response to amphetamine / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / Ras activation upon Ca2+ influx through NMDA receptor / cytoplasmic vesicle membrane / excitatory postsynaptic potential / regulation of membrane 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 / negative regulation of protein catabolic process / brain development / calcium ion transmembrane transport / visual learning / regulation of synaptic plasticity / response to wounding / long-term synaptic potentiation / memory / 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 / neuron projection / calmodulin binding / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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)69,3705
Polymers68,7152
Non-polymers6553
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-7 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.928, 90.013, 124.006
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, 255 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-A1BRA / 5-[(3-chlorobenzene-1-sulfonyl)methoxy]-6-methyl-N-[(pyridin-3-yl)methyl]pyrazine-2-carboxamide


Mass: 432.881 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H17ClN4O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 44.86 %
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: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.4→36.42 Å / Num. obs: 23262 / % possible obs: 94.2 % / Redundancy: 3.3 % / CC1/2: 0.986 / Rpim(I) all: 0.07948 / Net I/σ(I): 8.04
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.28 / Num. unique obs: 2048 / CC1/2: 0.724 / Rpim(I) all: 0.3087 / % possible all: 85.26

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia20.5.893data reduction
PHENIX1.20.1_4487phasing
xia20.5.893data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→36.42 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2524 1143 4.91 %
Rwork0.1966 --
obs0.1993 23256 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4286 0 44 252 4582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024418
X-RAY DIFFRACTIONf_angle_d0.465975
X-RAY DIFFRACTIONf_dihedral_angle_d4.737593
X-RAY DIFFRACTIONf_chiral_restr0.042666
X-RAY DIFFRACTIONf_plane_restr0.003771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.510.33861510.26012452X-RAY DIFFRACTION86
2.51-2.640.32391200.24812606X-RAY DIFFRACTION90
2.64-2.810.29571300.23832719X-RAY DIFFRACTION94
2.81-3.030.29291640.23222807X-RAY DIFFRACTION97
3.03-3.330.26131320.20212849X-RAY DIFFRACTION98
3.33-3.810.25331590.17842847X-RAY DIFFRACTION98
3.81-4.80.1971370.15452894X-RAY DIFFRACTION97
4.8-36.420.20061500.18052939X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4749-0.8276-0.2310.7234-0.20641.54240.1359-0.0059-0.3720.32010.0643-0.37980.26270.1094-0.0910.25990.0551-0.13840.2272-0.05540.37026.4114-21.709239.2959
20.8096-0.0389-0.74721.68990.01470.9780.1854-0.2975-0.28810.1628-0.08930.0142-0.1150.0074-0.01040.24670.0581-0.11410.2363-0.04080.43549.1505-16.825241.9245
31.45580.03190.83721.211-0.87981.284-0.1094-0.04620.15910.17560.0802-0.4397-0.10340.15170.01960.1571-0.0186-0.07920.1889-0.02580.24791.3388-7.466934.0122
41.74550.83910.08080.38980.08121.91890.0042-0.045-0.01740.2934-0.22810.0132-0.40880.08730.19840.26140.0551-0.07570.1337-0.04390.2358-11.2764-9.557233.335
52.2886-0.29040.03752.0498-0.04881.56150.0416-0.2238-0.15230.4264-0.01640.3506-0.0754-0.4379-0.02380.24830.03540.02690.3087-0.05320.3454-21.2569-10.258748.2394
63.03090.380.23811.3258-0.51132.2939-0.0893-0.5963-0.27360.46340.01390.08770.056-0.06830.07030.28270.041-0.00150.29180.01750.1806-14.4874-13.960248.8257
71.10470.2936-0.01642.1013-0.90383.2994-0.0891-0.1542-0.40570.24080.03250.39730.2179-0.64620.07130.17380.0505-0.00170.248-0.00390.2217-17.3944-19.490840.4912
81.23691.14430.53963.06290.9542.53110.00820.5077-0.1119-0.32670.1265-0.1661-0.20540.0967-0.06870.1505-0.01670.01110.2408-0.02590.2157-1.0391-9.493221.4578
91.54-1.27740.5971.37260.56396.30010.4385-0.1903-0.4231-0.27380.08460.18831.0106-0.4928-0.47920.2816-0.0641-0.05930.2502-0.00870.2892-5.4319-26.153529.6855
101.6431-1.2156-0.29572.6445-0.85792.9236-0.2518-0.14360.2607-0.2740.13640.2411-0.2146-0.25230.06390.17560.0945-0.09440.1785-0.01150.1663-26.9855-5.157310.5051
112.7412-0.21350.76272.69671.32645.73810.01650.0220.1895-0.1840.133-0.1457-0.8865-0.84720.07460.26460.0055-0.05140.23390.08070.2126-33.9623-4.61570.3027
121.4346-0.6220.54250.8864-0.37861.155-0.12810.05310.2427-0.02320.0917-0.1237-0.1887-0.04740.03720.1678-0.0084-0.01010.1447-0.01170.1359-20.1958-8.180510.4388
131.547-0.2756-1.01432.0957-0.41191.59130.0402-0.4414-0.2883-0.0329-0.16450.03910.37840.28930.10580.2618-0.00350.00550.26270.06050.1534-18.058-37.952114.1325
141.4132-1.2030.10813.68021.19291.8190.06390.32140.1087-0.68170.1588-0.43420.21740.1535-0.15710.1960.0065-0.01470.2087-0.02420.164-13.016-30.73317.9769
152.34540.4839-0.71423.46540.38832.0179-0.076-0.10020.02850.06930.02330.36920.1012-0.51520.00370.1587-0.0339-0.01950.18270.030.1702-28.8502-28.328315.3876
162.2005-0.3063-0.38352.73530.00881.67030.20230.12050.12710.3214-0.1357-0.3626-0.18360.2659-0.06890.1899-0.0407-0.12730.0923-0.00890.2523-14.0794-10.075316.8218
172.0753-0.0436-0.01911.84560.19471.8541-0.2756-0.55730.43760.60720.13230.1222-0.32-0.34750.02020.24450.14350.01790.3213-0.02740.1575-24.2708-6.610225.4051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 397 through 428 )
2X-RAY DIFFRACTION2chain 'A' and (resid 429 through 457 )
3X-RAY DIFFRACTION3chain 'A' and (resid 458 through 520 )
4X-RAY DIFFRACTION4chain 'A' and (resid 521 through 543 )
5X-RAY DIFFRACTION5chain 'A' and (resid 544 through 696 )
6X-RAY DIFFRACTION6chain 'A' and (resid 697 through 742 )
7X-RAY DIFFRACTION7chain 'A' and (resid 743 through 758 )
8X-RAY DIFFRACTION8chain 'A' and (resid 759 through 781 )
9X-RAY DIFFRACTION9chain 'A' and (resid 782 through 1001 )
10X-RAY DIFFRACTION10chain 'B' and (resid 403 through 420 )
11X-RAY DIFFRACTION11chain 'B' and (resid 421 through 448 )
12X-RAY DIFFRACTION12chain 'B' and (resid 449 through 538 )
13X-RAY DIFFRACTION13chain 'B' and (resid 539 through 688 )
14X-RAY DIFFRACTION14chain 'B' and (resid 689 through 708 )
15X-RAY DIFFRACTION15chain 'B' and (resid 709 through 753 )
16X-RAY DIFFRACTION16chain 'B' and (resid 754 through 771 )
17X-RAY DIFFRACTION17chain 'B' and (resid 772 through 1001 )

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