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- PDB-1pb8: CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH ... -

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Basic information

Entry
Database: PDB / ID: 1pb8
TitleCRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH D-SERINE AT 1.45 ANGSTROMS RESOLUTION
ComponentsN-methyl-D-aspartate Receptor Subunit 1
KeywordsLIGAND BINDING PROTEIN / Ligand binding receptor / rat / NR1
Function / homology
Function and homology information


pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane ...pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / transmitter-gated monoatomic ion channel activity / response to glycine / propylene metabolic process / Synaptic adhesion-like molecules / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / RAF/MAP kinase cascade / voltage-gated monoatomic cation channel activity / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / response to morphine / calcium ion transmembrane import into cytosol / glutamate binding / regulation of axonogenesis / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / regulation of synapse assembly / male mating behavior / glycine binding / positive regulation of reactive oxygen species biosynthetic process / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / suckling behavior / response to amine / startle response / social behavior / monoatomic cation transmembrane transport / associative learning / regulation of neuronal synaptic plasticity / cellular response to glycine / monoatomic cation transport / excitatory synapse / positive regulation of excitatory postsynaptic potential / positive regulation of dendritic spine maintenance / monoatomic ion channel complex / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / cellular response to manganese ion / glutamate receptor binding / synaptic cleft / prepulse inhibition / phosphatase binding / monoatomic cation channel activity / glutamate-gated receptor activity / calcium ion homeostasis / response to fungicide / regulation of neuron apoptotic process / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / sensory perception of pain / sodium ion transmembrane transport / response to amphetamine / ionotropic glutamate receptor signaling pathway / positive regulation of synaptic transmission, glutamatergic / hippocampal mossy fiber to CA3 synapse / adult locomotory behavior / learning / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / regulation of long-term neuronal synaptic plasticity / synaptic membrane / postsynaptic density membrane / terminal bouton / : / visual learning / cerebral cortex development / calcium ion transmembrane transport / regulation of synaptic plasticity / calcium channel activity / memory / neuron cellular homeostasis / intracellular calcium ion homeostasis / synaptic vesicle membrane / response to calcium ion / calcium ion transport / rhythmic process / synaptic vesicle / signaling receptor activity / amyloid-beta binding / presynaptic membrane / protein-containing complex assembly / chemical synaptic transmission / dendritic spine / negative regulation of neuron apoptotic process
Similarity search - Function
: / : / 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. ...: / : / 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 II / Periplasmic binding protein-like I / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-SERINE / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsFurukawa, H. / Gouaux, E.
CitationJournal: Embo J. / Year: 2003
Title: Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core
Authors: Furukawa, H. / Gouaux, E.
History
DepositionMay 14, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-methyl-D-aspartate Receptor Subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4322
Polymers33,3271
Non-polymers1051
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.460, 73.060, 96.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein N-methyl-D-aspartate Receptor Subunit 1


Mass: 33327.035 Da / Num. of mol.: 1 / Fragment: Ligand Binding Core
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: NMDAR1 / Organ: forebrain / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB (DE3) / References: UniProt: P35439
#2: Chemical ChemComp-DSN / D-SERINE


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 1000, sodium cacodylate, lithium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMsodium cacodylate1reservoirpH6.0
2100 mM1reservoirLi2SO4
320 %PEG10001reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. all: 52896 / Num. obs: 51309 / % possible obs: 97 % / Observed criterion σ(I): 14.06 / Biso Wilson estimate: 16.3 Å2
Reflection shellResolution: 1.45→1.5 Å / % possible all: 85.2
Reflection
*PLUS
Num. measured all: 414093 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 85.2 % / Rmerge(I) obs: 0.172

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.45→9.99 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 5105 10.1 %RANDOM
Rwork0.204 ---
all0.2041 51236 --
obs0.2041 50626 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.2052 Å2 / ksol: 0.465542 e/Å3
Displacement parametersBiso mean: 17.8 Å2
Refine analyzeLuzzati coordinate error free: 0.19 Å / Luzzati sigma a free: 0.08 Å
Refinement stepCycle: LAST / Resolution: 1.45→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2171 0 7 353 2531
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 1.45→1.54 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 740 10.1 %
Rwork0.218 6571 -
obs-6571 84.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DS.PARAMDS.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.17
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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