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

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Basic information

Entry
Database: PDB / ID: 3qel
TitleCrystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with ifenprodil
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 corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / cellular response to curcumin / regulation of cAMP/PKA signal transduction / auditory behavior / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to carbohydrate / fear response ...cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / cellular response to curcumin / regulation of cAMP/PKA signal transduction / auditory behavior / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to carbohydrate / fear response / sensitization / suckling behavior / response to other organism / response to methylmercury / response to hydrogen sulfide / dendritic branch / regulation of ARF protein signal transduction / apical dendrite / response to manganese ion / response to glycoside / interleukin-1 receptor binding / cellular response to dsRNA / cellular response to lipid / response to growth hormone / RAF/MAP kinase cascade / positive regulation of inhibitory postsynaptic potential / heterocyclic compound binding / negative regulation of dendritic spine maintenance / response to amine / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / response to zinc ion / NMDA selective glutamate receptor complex / glutamate binding / ligand-gated sodium channel activity / positive regulation of glutamate secretion / calcium ion transmembrane import into cytosol / startle response / protein heterotetramerization / small molecule binding / glycine binding / receptor clustering / behavioral response to pain / parallel fiber to Purkinje cell synapse / behavioral fear response / regulation of neuronal synaptic plasticity / associative learning / regulation of postsynaptic membrane potential / regulation of MAPK cascade / action potential / response to electrical stimulus / extracellularly glutamate-gated ion channel activity / neuron development / multicellular organismal response to stress / monoatomic cation transmembrane transport / detection of mechanical stimulus involved in sensory perception of pain / response to magnesium ion / response to mechanical stimulus / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transport / glutamate receptor binding / ligand-gated monoatomic ion channel activity / long-term memory / postsynaptic density, intracellular component / synaptic cleft / response to fungicide / monoatomic cation channel activity / cellular response to manganese ion / glutamate-gated receptor activity / regulation of long-term synaptic depression / positive regulation of synaptic transmission, glutamatergic / response to cytokine / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / cell adhesion molecule binding / D2 dopamine receptor binding / response to amphetamine / ionotropic glutamate receptor signaling pathway / ionotropic glutamate receptor binding / learning / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / protein tyrosine kinase binding / excitatory postsynaptic potential / hippocampus development / cellular response to forskolin / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / cellular response to amino acid stimulus / protein serine/threonine kinase binding / sodium ion transmembrane transport / response to nicotine / synaptic membrane / response to cocaine / regulation of long-term neuronal synaptic plasticity / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / cerebral cortex development / response to calcium ion
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 / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site ...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 / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / 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)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.3Oct 12, 2011Group: Derived calculations
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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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.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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_label_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_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 27, 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)171,68115
Polymers168,6004
Non-polymers3,08111
Water2,468137
1
A: NMDA glutamate receptor subunit
B: Glutamate [NMDA] receptor subunit epsilon-2
D: Glutamate [NMDA] receptor subunit epsilon-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,50512
Polymers125,6683
Non-polymers2,8379
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-7 kcal/mol
Surface area29000 Å2
MethodPISA
2
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)127,44811
Polymers125,6683
Non-polymers1,7808
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-21 kcal/mol
Surface area28090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)267.993, 60.869, 144.923
Angle α, β, γ (deg.)90.00, 116.49, 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, 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)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-3]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-1-3-4-4/a3-b1_a4-c1_c4-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-L-Fucp]{}[(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, 141 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.: 137 / 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: 3.14 Å3/Da / Density % sol: 60.8 %
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: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 21, 2010
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 64034 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.51 / Rsym value: 0.51 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID% possible all
2.6-2.690.51195.9
2.69-2.80.439199.1
2.8-2.930.33199.2
2.93-3.080.214199
3.08-3.280.143199.2
3.28-3.530.095199
3.53-3.880.07199.1
3.88-4.450.056198.8
4.45-5.60.051198.2
5.6-500.037196.6

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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: 2.6→29.983 Å / SU ML: 0.32 / σ(F): 0 / Phase error: 26.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2381 3051 5.1 %
Rwork0.1879 --
obs0.1904 59854 92.03 %
all-59854 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.061 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.2611 Å2-0 Å2-9.9517 Å2
2--15.4745 Å2-0 Å2
3----8.2134 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10395 0 205 137 10737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110870
X-RAY DIFFRACTIONf_angle_d1.13414835
X-RAY DIFFRACTIONf_dihedral_angle_d15.7843769
X-RAY DIFFRACTIONf_chiral_restr0.0721768
X-RAY DIFFRACTIONf_plane_restr0.0041880
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.64060.326990.28082085X-RAY DIFFRACTION73
2.6406-2.68390.35651350.28232117X-RAY DIFFRACTION78
2.6839-2.73010.41451070.28112246X-RAY DIFFRACTION81
2.7301-2.77970.34141210.28542377X-RAY DIFFRACTION84
2.7797-2.83320.31751100.25362364X-RAY DIFFRACTION85
2.8332-2.89090.32551490.25612444X-RAY DIFFRACTION88
2.8909-2.95380.29241280.24942480X-RAY DIFFRACTION90
2.9538-3.02240.31831560.23852546X-RAY DIFFRACTION91
3.0224-3.09790.28981500.22132572X-RAY DIFFRACTION93
3.0979-3.18160.26991160.19882624X-RAY DIFFRACTION93
3.1816-3.27510.27831260.20432666X-RAY DIFFRACTION95
3.2751-3.38070.24031520.20452677X-RAY DIFFRACTION96
3.3807-3.50130.26111440.1892705X-RAY DIFFRACTION97
3.5013-3.64130.25231300.18222731X-RAY DIFFRACTION98
3.6413-3.80670.22781630.17152776X-RAY DIFFRACTION98
3.8067-4.0070.20521700.15612691X-RAY DIFFRACTION98
4.007-4.25730.20661410.14522769X-RAY DIFFRACTION98
4.2573-4.5850.15041220.13352799X-RAY DIFFRACTION98
4.585-5.04440.18671580.13532782X-RAY DIFFRACTION98
5.0444-5.76990.23211660.17762742X-RAY DIFFRACTION98
5.7699-7.25240.25161560.21232769X-RAY DIFFRACTION97
7.2524-29.98460.20521520.19332841X-RAY DIFFRACTION96
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)
10.8059-0.26340.47730.4796-0.03271.8209-0.0522-0.04160.0551-0.0076-0.04910.0488-0.1159-0.041400.26-0.0240.01330.1776-0.02760.290885.5566.7972-53.0625
20.85030.20090.28241.42310.26071.4876-0.1579-0.18670.04870.15710.10120.0336-0.2439-0.1876-00.34940.05320.01520.35670.00110.252781.389915.1826-21.2092
31.22250.56860.56730.52750.2081.1072-0.0180.20240.01810.18310.0640.14080.04180.168200.49590.0758-0.00540.43090.22930.513622.6335-1.8055-11.4271
40.5391-0.09050.12410.5892-0.37921.0387-0.06820.2377-0.0948-0.1280.17120.0328-0.06950.0926-00.38870.00660.00220.71140.00980.462925.19143.2417-43.9746
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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