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- PDB-2a5t: Crystal Structure Of The NR1/NR2A ligand-binding cores complex -

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Basic information

Entry
Database: PDB / ID: 2a5t
TitleCrystal Structure Of The NR1/NR2A ligand-binding cores complex
Components
  • N-methyl-D-aspartate receptor NMDAR1-4a subunit
  • N-methyl-D-aspartate receptor NMDAR2A subunit
KeywordsMETAL TRANSPORT / MEMBRANE PROTEIN / Protein-ligand complex
Function / homology
Function and homology information


neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / pons maturation / response to environmental enrichment / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / pons maturation / response to environmental enrichment / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / auditory behavior / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / olfactory learning / conditioned taste aversion / serotonin metabolic process / dendritic branch / regulation of respiratory gaseous exchange / response to other organism / protein localization to postsynaptic membrane / regulation of ARF protein signal transduction / cellular response to magnesium ion / transmitter-gated monoatomic ion channel activity / positive regulation of inhibitory postsynaptic potential / response to methylmercury / sleep / response to glycine / propylene metabolic process / response to carbohydrate / dendritic spine organization / response to manganese ion / locomotion / regulation of NMDA receptor activity / cellular response to dsRNA / response to glycoside / cellular response to lipid / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / voltage-gated monoatomic cation channel activity / neurotransmitter receptor complex / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / glutamate binding / response to morphine / glutamate receptor signaling pathway / regulation of axonogenesis / calcium ion transmembrane import into cytosol / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / glycine binding / regulation of synapse assembly / spinal cord development / response to amine / parallel fiber to Purkinje cell synapse / suckling behavior / cellular response to zinc ion / startle response / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / dopamine metabolic process / response to lithium ion / positive regulation of calcium ion transport into cytosol / modulation of excitatory postsynaptic potential / response to light stimulus / regulation of postsynaptic membrane potential / regulation of neuron apoptotic process / action potential / associative learning / cellular response to glycine / monoatomic cation transport / conditioned place preference / excitatory synapse / social behavior / positive regulation of dendritic spine maintenance / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / positive regulation of protein targeting to membrane / positive regulation of excitatory postsynaptic potential / cellular response to manganese ion / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / multicellular organismal response to stress / synaptic cleft / neuron development / prepulse inhibition / postsynaptic density, intracellular component / phosphatase binding / monoatomic cation channel activity / calcium ion homeostasis / response to fungicide / glutamate-gated receptor activity / cell adhesion molecule binding / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / neurogenesis
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / 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 / : / : / 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
GLUTAMIC ACID / GLYCINE / : / : / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Canis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFurukawa, H. / Singh, S.K. / Mancusso, R. / Gouaux, E.
CitationJournal: Nature / Year: 2005
Title: Subunit arrangement and function in NMDA receptors
Authors: Furukawa, H. / Singh, S.K. / Mancusso, R. / Gouaux, E.
History
DepositionJun 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 NMDAR1-4a subunit
B: N-methyl-D-aspartate receptor NMDAR2A subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4154
Polymers65,1922
Non-polymers2222
Water6,161342
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.640, 89.989, 126.116
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 NMDAR1-4a subunit / NMDA receptor NR1 subunit


Mass: 33340.031 Da / Num. of mol.: 1 / Fragment: S1S2 ligand-binding core
Source method: isolated from a genetically manipulated source
Details: construct of residues 394-544 and 663-800 of GB AAB50932
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Canis lupus familiaris (dog)
Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB (DE3) / References: UniProt: P35439, GenBank: 475566
#2: Protein N-methyl-D-aspartate receptor NMDAR2A subunit / NMDA receptor NR2A subunit / NMDA receptor NMDAR2A subunit / glutamate receptor / ionotropic / N- ...NMDA receptor NR2A subunit / NMDA receptor NMDAR2A subunit / glutamate receptor / ionotropic / N-methyl D-aspartate 2A


Mass: 31852.391 Da / Num. of mol.: 1 / Fragment: S1S2 ligand-binding core
Source method: isolated from a genetically manipulated source
Details: construct of residues 401-539 and 661-802 of GB AAB58801
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): OrigamiB (DE3) / References: UniProt: Q00959, GenBank: 2155310
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.38 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 7
Details: PEG 8000, HEPES, Calcium acetate, pH 7., EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.01 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2004
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 44066 / Num. obs: 44066 / % possible obs: 86.5 % / Biso Wilson estimate: 16.6 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1836296.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.253 4011 10.1 %RANDOM
Rwork0.213 ---
obs0.214 39898 93.2 %-
all-44066 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.1972 Å2 / ksol: 0.350687 e/Å3
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4171 0 15 342 4528
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 480 10.1 %
Rwork0.242 4281 -
obs--68.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2lig.paramlig.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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