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- PDB-5ewj: CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR ... -

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Basic information

Entry
Database: PDB / ID: 5ewj
TitleCRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH IFENPRODIL
Components
  • Glutamate receptor ionotropic, NMDA 2B
  • NMDA glutamate receptor subunit
KeywordsTRANSPORT PROTEIN / Glutamate receptor / allosteric modulator / GluN2B antagonists
Function / homology
Function and homology information


excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / Neurexins and neuroligins / ligand-gated sodium channel activity ...excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / Neurexins and neuroligins / ligand-gated sodium channel activity / glutamate binding / glutamate receptor signaling pathway / response to zinc ion / calcium ion transmembrane import into cytosol / protein heterotetramerization / glycine binding / monoatomic cation transmembrane transport / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Long-term potentiation / regulation of neuronal synaptic plasticity / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / MECP2 regulates neuronal receptors and channels / glutamate-gated calcium ion channel activity / EPHB-mediated forward signaling / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / excitatory postsynaptic potential / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / brain development / calcium ion transmembrane transport / regulation of synaptic plasticity / long-term synaptic potentiation / late endosome / signaling receptor activity / amyloid-beta binding / RAF/MAP kinase cascade / response to ethanol / chemical synaptic transmission / postsynaptic membrane / learning or memory / cytoskeleton / neuron projection / lysosome / postsynaptic density / dendrite / synapse / endoplasmic reticulum membrane / cell surface / zinc ion binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Response regulator / 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 / : / : / Response regulator / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-QEL / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.77 Å
AuthorsPandit, J.
CitationJournal: Mol.Pharmacol. / Year: 2016
Title: A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B-selective Antagonists.
Authors: Stroebel, D. / Buhl, D.L. / Knafels, J.D. / Chanda, P.K. / Green, M. / Sciabola, S. / Mony, L. / Paoletti, P. / Pandit, J.
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / citation / diffrn_radiation_wavelength / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NMDA glutamate receptor subunit
B: Glutamate receptor ionotropic, NMDA 2B
C: NMDA glutamate receptor subunit
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,15515
Polymers170,2204
Non-polymers2,93511
Water6,323351
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A: NMDA glutamate receptor subunit
B: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0338
Polymers85,1102
Non-polymers1,9236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-20 kcal/mol
Surface area28880 Å2
MethodPISA
2
C: NMDA glutamate receptor subunit
D: Glutamate receptor ionotropic, NMDA 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1227
Polymers85,1102
Non-polymers1,0125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-20 kcal/mol
Surface area29260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.460, 60.100, 145.000
Angle α, β, γ (deg.)90.000, 116.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein NMDA glutamate receptor subunit


Mass: 43757.977 Da / Num. of mol.: 2 / Fragment: Amino Terminal Domain (UNP residues 23-408) / Mutation: N61Q,N371Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: grin1, NR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q91977, UniProt: A0A1L8F5J9*PLUS
#2: Protein Glutamate receptor ionotropic, NMDA 2B / GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / ...GluN2B / Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / NR2B / N-methyl-D-aspartate receptor subunit 3 / hNR3


Mass: 41351.902 Da / Num. of mol.: 2 / Fragment: Amino Terminal Domain (UNP residues 31-394) / Mutation: N348D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN2B, NMDAR2B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13224

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Sugars , 2 types, 7 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 355 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-QEL / 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol / Ifenprodil


Mass: 325.445 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 3.6M Na Formate, 0.1 M Hepes pH 7.0 / PH range: 6.8-7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→120.42 Å / Num. obs: 53122 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 78.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Net I/σ(I): 17 / Num. measured all: 177049
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.77-3.913.40.1468.3116766343560.9810.09399.7
3.91-120.423.20.02833.160283187660.9990.01997.6

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.6refinement
Aimless0.3.5data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3QEL

3qel


Resolution: 2.77→27.92 Å / Cor.coef. Fo:Fc: 0.9407 / Cor.coef. Fo:Fc free: 0.9261 / SU R Cruickshank DPI: 0.638 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.627 / SU Rfree Blow DPI: 0.269 / SU Rfree Cruickshank DPI: 0.274
RfactorNum. reflection% reflectionSelection details
Rfree0.2112 2685 5.08 %RANDOM
Rwork0.1742 ---
obs0.1761 52883 98.94 %-
Displacement parametersBiso max: 177.76 Å2 / Biso mean: 75.14 Å2 / Biso min: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.6808 Å20 Å211.8071 Å2
2---8.8446 Å20 Å2
3---3.1638 Å2
Refine analyzeLuzzati coordinate error obs: 0.311 Å
Refinement stepCycle: final / Resolution: 2.77→27.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11017 0 194 351 11562
Biso mean--93.25 68.26 -
Num. residues----1421
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3912SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes266HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1673HARMONIC5
X-RAY DIFFRACTIONt_it11466HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1605SEMIHARMONIC5
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_contact12891SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11466HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg15613HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.02
X-RAY DIFFRACTIONt_other_torsion20.53
LS refinement shellResolution: 2.77→2.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2695 206 5.23 %
Rwork0.2234 3735 -
all0.2257 3941 -
obs--99.72 %
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)
11.241-0.35240.19530.9856-0.27022.2563-0.07260.04580.09880.0246-0.0150.0334-0.1318-0.01120.0876-0.111-0.05380.0241-0.1414-0.0343-0.073185.78517.0621-54.0168
21.73760.48670.47651.81010.22822.5867-0.1418-0.33280.1720.2525-0.02780.1446-0.4067-0.26120.1696-0.0580.06560.0107-0.1177-0.0565-0.201580.873314.9138-20.9994
32.18770.47151.11372.17060.35932.17660.1029-0.0289-0.1760.4976-0.07590.18150.1488-0.1035-0.027-0.11250.05510.0212-0.15590.2086-0.14422.6556-2.2073-11.0039
42.7359-0.12480.95871.0969-0.38661.6067-0.05270.5062-0.1979-0.11780.172-0.0065-0.06480.2447-0.1194-0.2390.0370.00610.1762-0.0268-0.141825.47643.3498-44.3376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A23 - 407
2X-RAY DIFFRACTION2{ B|* }B32 - 393
3X-RAY DIFFRACTION3{ C|* }C23 - 407
4X-RAY DIFFRACTION4{ D|* }D32 - 394

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