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- PDB-3jpy: Crystal structure of the zinc-bound amino terminal domain of the ... -

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Basic information

Entry
Database: PDB / ID: 3jpy
TitleCrystal structure of the zinc-bound 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 / sensitization / regulation of cAMP/PKA signal transduction / EPHB-mediated forward signaling / auditory behavior / Assembly and cell surface presentation of NMDA receptors / dendritic branch ...cellular response to curcumin / cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / sensitization / regulation of cAMP/PKA signal transduction / EPHB-mediated forward signaling / auditory behavior / Assembly and cell surface presentation of NMDA receptors / dendritic branch / response to hydrogen sulfide / response to other organism / positive regulation of inhibitory postsynaptic potential / apical dendrite / regulation of ARF protein signal transduction / response to methylmercury / fear response / response to carbohydrate / cellular response to dsRNA / interleukin-1 receptor binding / negative regulation of dendritic spine maintenance / cellular response to lipid / positive regulation of glutamate secretion / response to growth hormone / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / RAF/MAP kinase cascade / response to manganese ion / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / glutamate binding / protein heterotetramerization / heterocyclic compound binding / glycine binding / receptor clustering / parallel fiber to Purkinje cell synapse / suckling behavior / regulation of postsynaptic membrane potential / response to amine / small molecule binding / startle response / monoatomic cation transmembrane transport / associative learning / : / behavioral response to pain / response to magnesium ion / regulation of MAPK cascade / regulation of neuronal synaptic plasticity / action potential / extracellularly glutamate-gated ion channel activity / monoatomic cation transport / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / cellular response to manganese ion / behavioral fear response / postsynaptic density, intracellular component / glutamate receptor binding / neuron development / synaptic cleft / multicellular organismal response to stress / detection of mechanical stimulus involved in sensory perception of pain / response to electrical stimulus / monoatomic cation channel activity / glutamate-gated receptor activity / response to mechanical stimulus / response to fungicide / D2 dopamine receptor binding / cell adhesion molecule binding / ionotropic glutamate receptor binding / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cellular response to forskolin / response to amphetamine / response to cytokine / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / hippocampal mossy fiber to CA3 synapse / protein tyrosine kinase binding / hippocampus development / learning / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / cellular response to amino acid stimulus / response to nicotine / response to cocaine / regulation of long-term neuronal synaptic plasticity / synaptic membrane / response to lead ion / postsynaptic density membrane / terminal bouton / : / cellular response to growth factor stimulus / beta-catenin binding / cerebral cortex development / regulation of synaptic plasticity / calcium channel activity
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 / MOLECULAR REPLACEMENT / Resolution: 3.209 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 1.2Jul 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_conn_type / 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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 27, 2024Group: Structure summary / Category: 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)42,25114
Polymers41,2811
Non-polymers97013
Water1086
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)84,50128
Polymers82,5622
Non-polymers1,93926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4780 Å2
ΔGint-375 kcal/mol
Surface area29850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.368, 143.368, 88.467
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Sugars , 2 types, 3 molecules A

#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

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Non-polymers , 4 types, 17 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / 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: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 6.36 Å3/Da / Density % sol: 80.65 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 3.3M NaCl, 2% PEG400, 0.1M MgCl2, 0.1M acetate, 0.1mM ZnCl2, 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: 1.2826 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: 1.2826 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 17197 / % possible obs: 98.4 % / Biso Wilson estimate: 114.64 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 16.8
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 3.1 / % possible all: 94.4

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3JPW

3jpw


Resolution: 3.209→29.29 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.7 / σ(F): 1.48 / Phase error: 26.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 859 5.02 %
Rwork0.2042 --
obs0.2056 17128 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 94.865 Å2 / ksol: 0.289 e/Å3
Displacement parametersBiso mean: 114.767 Å2
Baniso -1Baniso -2Baniso -3
1--22.374 Å2-0 Å20 Å2
2---22.374 Å20 Å2
3---44.749 Å2
Refinement stepCycle: LAST / Resolution: 3.209→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 39 6 2651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072711
X-RAY DIFFRACTIONf_angle_d1.0413712
X-RAY DIFFRACTIONf_dihedral_angle_d17.334882
X-RAY DIFFRACTIONf_chiral_restr0.063443
X-RAY DIFFRACTIONf_plane_restr0.004471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.209-3.41020.38081370.30882600X-RAY DIFFRACTION95
3.4102-3.6730.28471550.25782704X-RAY DIFFRACTION99
3.673-4.04180.27541440.20382677X-RAY DIFFRACTION99
4.0418-4.62470.16591510.16032737X-RAY DIFFRACTION99
4.6247-5.81910.20911420.17112744X-RAY DIFFRACTION99
5.8191-29.29070.23381300.21452807X-RAY DIFFRACTION98

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