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- PDB-3jpw: Crystal structure of amino terminal domain of the NMDA receptor s... -

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Basic information

Entry
Database: PDB / ID: 3jpw
TitleCrystal structure of amino terminal domain of the NMDA receptor subunit NR2B
ComponentsGlutamate [NMDA] receptor subunit epsilon-2
KeywordsTRANSPORT PROTEIN / NMDA receptor / amino terminal domain / phenylethanolamine / Cell junction / Cell membrane / Glycoprotein / Ion transport / Ionic channel / Magnesium / Membrane / Phosphoprotein / Postsynaptic cell membrane / Receptor / Synapse / Transmembrane / Transport
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 / glutamate binding / 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 / 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 / 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 / regulation of synaptic plasticity / cellular response to growth factor stimulus / calcium channel activity / response to toxic substance
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 / : / Ionotropic glutamate receptor ...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
Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.803 Å
AuthorsKarakas, E. / Simorowski, N. / Furukawa, H.
CitationJournal: Embo J. / Year: 2009
Title: Structure of the zinc-bound amino-terminal domain of the NMDA receptor NR2B subunit.
Authors: Karakas, E. / Simorowski, N. / Furukawa, H.
History
DepositionSep 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 13, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate [NMDA] receptor subunit epsilon-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,34921
Polymers41,2811
Non-polymers1,06820
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glutamate [NMDA] receptor subunit epsilon-2
hetero molecules

A: Glutamate [NMDA] receptor subunit epsilon-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,69842
Polymers82,5622
Non-polymers2,13640
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area7870 Å2
ΔGint-356 kcal/mol
Surface area28780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.975, 142.975, 89.263
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Glutamate [NMDA] receptor subunit epsilon-2 / N-methyl D-aspartate receptor subtype 2B / NMDAR2B / NR2B


Mass: 41280.820 Da / Num. of mol.: 1 / Fragment: Amino terminal domain / 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
#2: 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.: 2
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
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3.3M NaCl, 2% PEG400, 0.1M MgCl2, 0.1M acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 6, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 25955 / % possible obs: 99.2 % / Biso Wilson estimate: 82.12 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 16.4
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.767 / Mean I/σ(I) obs: 2.1 / % possible all: 93.6

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Phasing

PhasingMethod: MIRAS

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Processing

Software
NameVersionClassificationNB
SHARPphasing
SOLOMONphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.803→28.931 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.78 / σ(F): 1.34 / Phase error: 27.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2312 1338 5.17 %
Rwork0.1968 --
obs0.1986 25898 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.136 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso mean: 92.215 Å2
Baniso -1Baniso -2Baniso -3
1--19.84 Å20 Å20 Å2
2---19.84 Å20 Å2
3---39.68 Å2
Refinement stepCycle: LAST / Resolution: 2.803→28.931 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2772 0 46 18 2836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092879
X-RAY DIFFRACTIONf_angle_d1.2183933
X-RAY DIFFRACTIONf_dihedral_angle_d19.3781009
X-RAY DIFFRACTIONf_chiral_restr0.077458
X-RAY DIFFRACTIONf_plane_restr0.004499
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.803-2.90310.31981290.32542291X-RAY DIFFRACTION94
2.9031-3.01930.34991360.3022400X-RAY DIFFRACTION99
3.0193-3.15650.29281410.28312429X-RAY DIFFRACTION100
3.1565-3.32270.32651380.23692483X-RAY DIFFRACTION100
3.3227-3.53050.25711380.21522435X-RAY DIFFRACTION100
3.5305-3.80260.23651350.19542464X-RAY DIFFRACTION100
3.8026-4.18420.18751400.15712472X-RAY DIFFRACTION100
4.1842-4.78730.15571300.14372481X-RAY DIFFRACTION100
4.7873-6.02260.19641360.16872514X-RAY DIFFRACTION100
6.0226-28.93230.25651150.21032591X-RAY DIFFRACTION99

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