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- PDB-3qem: Crystal structure of amino terminal domains of the NMDA receptor ... -

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Basic information

Entry
Database: PDB / ID: 3qem
TitleCrystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with Ro 25-6981
Components
  • Glutamate [NMDA] receptor subunit epsilon-2
  • NMDA glutamate receptor subunit
KeywordsTRANSPORT PROTEIN / ion channel / NMDA receptor / allosteric modulation / phenylethanolamine / N-Glycosylation / extracellular / transmembrane
Function / homology
Function and homology information


cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / regulation of cAMP/PKA signal transduction / EPHB-mediated forward signaling / sensitization / auditory behavior / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide ...cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / regulation of cAMP/PKA signal transduction / EPHB-mediated forward signaling / sensitization / auditory behavior / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / dendritic branch / response to other organism / regulation of ARF protein signal transduction / fear response / apical dendrite / positive regulation of inhibitory postsynaptic potential / response to methylmercury / response to carbohydrate / response to manganese ion / interleukin-1 receptor binding / cellular response to dsRNA / response to glycoside / positive regulation of glutamate secretion / negative regulation of dendritic spine maintenance / cellular response to lipid / response to growth hormone / regulation of monoatomic cation transmembrane transport / heterocyclic compound binding / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / glutamate binding / response to zinc ion / calcium ion transmembrane import into cytosol / protein heterotetramerization / glycine binding / response to amine / parallel fiber to Purkinje cell synapse / receptor clustering / small molecule binding / suckling behavior / regulation of long-term synaptic depression / startle response / monoatomic cation transmembrane transport / behavioral response to pain / response to magnesium ion / associative learning / regulation of postsynaptic membrane potential / regulation of MAPK cascade / action potential / extracellularly glutamate-gated ion channel activity / monoatomic cation transport / positive regulation of excitatory postsynaptic potential / response to electrical stimulus / regulation of neuronal synaptic plasticity / cellular response to manganese ion / long-term memory / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / response to mechanical stimulus / behavioral fear response / detection of mechanical stimulus involved in sensory perception of pain / multicellular organismal response to stress / synaptic cleft / neuron development / postsynaptic density, intracellular component / monoatomic cation channel activity / response to fungicide / glutamate-gated receptor activity / D2 dopamine receptor binding / cell adhesion molecule binding / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / response to cytokine / ionotropic glutamate receptor binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / sodium ion transmembrane transport / cellular response to forskolin / response to amphetamine / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / protein tyrosine kinase binding / hippocampal mossy fiber to CA3 synapse / hippocampus development / excitatory postsynaptic potential / regulation of membrane potential / learning / response to nicotine / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cellular response to amino acid stimulus / response to cocaine / synaptic membrane / response to lead ion / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / cerebral cortex development / beta-catenin binding
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-QEM / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.003 Å
AuthorsKarakas, E. / Simorowski, N. / Furukawa, H.
CitationJournal: Nature / Year: 2011
Title: Subunit arrangement and phenylethanolamine binding in GluN1/GluN2B NMDA receptors.
Authors: Karakas, E. / Simorowski, N. / Furukawa, H.
History
DepositionJan 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _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.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 16, 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 [NMDA] receptor subunit epsilon-2
C: NMDA glutamate receptor subunit
D: Glutamate [NMDA] receptor subunit epsilon-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,34214
Polymers168,6004
Non-polymers2,74210
Water00
1
A: NMDA glutamate receptor subunit
B: Glutamate [NMDA] receptor subunit epsilon-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2378
Polymers84,3002
Non-polymers1,9376
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-9 kcal/mol
Surface area29110 Å2
MethodPISA
2
C: NMDA glutamate receptor subunit
D: Glutamate [NMDA] receptor subunit epsilon-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1056
Polymers84,3002
Non-polymers8054
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-24 kcal/mol
Surface area27910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)268.029, 61.255, 144.423
Angle α, β, γ (deg.)90.00, 116.32, 90.00
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: 42932.055 Da / Num. of mol.: 2 / Fragment: Amino Terminal Domain, residues 23-405 / Mutation: N61Q, N371Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: grin1, NR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q91977, UniProt: A0A1L8F5J9*PLUS
#2: Protein Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / NMDAR2B / NR2B


Mass: 41367.902 Da / Num. of mol.: 2 / Fragment: Amino Terminal Domain, residues 31-394 / Mutation: N348D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2b / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q00960

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Sugars , 2 types, 6 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
#4: 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.: 5
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 , 2 types, 4 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-QEM / 4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol


Mass: 339.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H29NO2

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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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 3.0-3.5M NaFormate, 0.1 M HEPES pH 7.5 , VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 18, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 42325 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
3-3.110.633195.6
3.11-3.230.482198.6
3.23-3.380.326198.7
3.38-3.560.225198.8
3.56-3.780.142198.8
3.78-4.070.097198.6
4.07-4.480.064198.5
4.48-5.130.055198
5.13-6.460.059197.5
6.46-500.034195.3

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JPW, 3QEK

3jpw

3qek


Resolution: 3.003→29.941 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2501 2031 5.06 %
Rwork0.1915 --
obs0.1945 40132 94.35 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.96 Å2 / ksol: 0.296 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.953 Å2-0 Å2-10.9331 Å2
2--17.7122 Å2-0 Å2
3----9.7592 Å2
Refinement stepCycle: LAST / Resolution: 3.003→29.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10090 0 183 0 10273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110517
X-RAY DIFFRACTIONf_angle_d1.23514390
X-RAY DIFFRACTIONf_dihedral_angle_d15.0483510
X-RAY DIFFRACTIONf_chiral_restr0.0721738
X-RAY DIFFRACTIONf_plane_restr0.0051827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0034-3.07320.3781140.30472130X-RAY DIFFRACTION79
3.0732-3.150.36061170.27642285X-RAY DIFFRACTION88
3.15-3.23510.3161060.25082391X-RAY DIFFRACTION88
3.2351-3.33020.361230.22982402X-RAY DIFFRACTION90
3.3302-3.43750.31491330.232455X-RAY DIFFRACTION92
3.4375-3.56020.29191230.20342502X-RAY DIFFRACTION94
3.5602-3.70250.27981290.1862558X-RAY DIFFRACTION95
3.7025-3.87060.25091660.16892554X-RAY DIFFRACTION97
3.8706-4.07420.22191520.15522647X-RAY DIFFRACTION98
4.0742-4.32880.23021280.14342649X-RAY DIFFRACTION99
4.3288-4.66190.16931250.13812678X-RAY DIFFRACTION99
4.6619-5.12890.19831520.14342674X-RAY DIFFRACTION99
5.1289-5.86620.25241590.20892654X-RAY DIFFRACTION99
5.8662-7.37250.29341510.23162718X-RAY DIFFRACTION99
7.3725-29.94240.21521530.20452804X-RAY DIFFRACTION99
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)
11.0848-0.26140.32110.77660.14981.6131-0.0377-0.02280.0653-0.0378-0.06750.0435-0.0833-0.002800.2532-0.03750.03140.1669-0.03440.286185.27496.6402-52.9787
20.9737-0.07690.26941.13870.08891.5597-0.1364-0.11110.06350.18080.08860.0067-0.2289-0.059700.26260.07820.01590.2636-0.00470.203881.32415.3128-21.2482
31.33050.49960.61790.6021-0.12381.014-0.0030.1513-0.03680.19840.06820.1043-0.00630.153700.47620.02260.01250.38690.24430.509422.8048-1.634-11.138
40.6462-0.0045-0.0360.52-0.57731.2684-0.14080.1797-0.1226-0.15780.24520.0177-0.0940.0362-00.4221-0.0063-0.01730.5721-0.0230.483824.94333.2428-43.6723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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