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- PDB-2a5s: Crystal Structure Of The NR2A Ligand Binding Core In Complex With... -

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Basic information

Entry
Database: PDB / ID: 2a5s
TitleCrystal Structure Of The NR2A Ligand Binding Core In Complex With Glutamate
ComponentsN-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 / response to hydrogen sulfide / positive regulation of inhibitory postsynaptic potential / directional locomotion / response to environmental enrichment / regulation of ARF protein signal transduction / response to methylmercury ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / response to hydrogen sulfide / positive regulation of inhibitory postsynaptic potential / directional locomotion / response to environmental enrichment / regulation of ARF protein signal transduction / response to methylmercury / response to other organism / Assembly and cell surface presentation of NMDA receptors / serotonin metabolic process / response to carbohydrate / cellular response to dsRNA / cellular response to lipid / cellular response to magnesium ion / protein localization to postsynaptic membrane / conditioned place preference / sleep / locomotion / dendritic spine organization / response to manganese ion / regulation of monoatomic cation transmembrane transport / voltage-gated monoatomic cation channel activity / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / regulation of NMDA receptor activity / parallel fiber to Purkinje cell synapse / NMDA selective glutamate receptor complex / cellular response to zinc ion / calcium ion transmembrane import into cytosol / glutamate binding / glutamate receptor signaling pathway / spinal cord development / action potential / startle response / response to amine / dopamine metabolic process / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / response to lithium ion / modulation of excitatory postsynaptic potential / regulation of postsynaptic membrane potential / positive regulation of excitatory postsynaptic potential / cellular response to glycine / postsynaptic density, intracellular component / response to light stimulus / positive regulation of protein targeting to membrane / multicellular organismal response to stress / neuron development / Unblocking of NMDA receptors, glutamate binding and activation / cellular response to manganese ion / glutamate receptor binding / monoatomic cation channel activity / glutamate-gated receptor activity / cell adhesion molecule binding / response to fungicide / glutamate-gated calcium ion channel activity / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / sensory perception of pain / response to amphetamine / ionotropic glutamate receptor signaling pathway / protein tyrosine kinase binding / neurogenesis / positive regulation of synaptic transmission, glutamatergic / regulation of membrane potential / excitatory postsynaptic potential / learning / response to cocaine / synaptic transmission, glutamatergic / hippocampus development / synaptic membrane / long-term synaptic potentiation / response to nicotine / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cellular response to amino acid stimulus / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / modulation of chemical synaptic transmission / visual learning / cytoplasmic vesicle membrane / protein catabolic process / calcium channel activity / regulation of synaptic plasticity / negative regulation of protein catabolic process / terminal bouton / cellular response to growth factor stimulus / response to organic cyclic compound / cerebral cortex development / memory / response to wounding / response to calcium ion / calcium-dependent protein binding / calcium ion transport / rhythmic process / synaptic vesicle / presynaptic membrane / ATPase binding
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 / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...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 / : / Glutamate receptor ionotropic, NMDA 2A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Combination of molecular replacement, SAD / Resolution: 1.7 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 1.4Oct 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: N-methyl-D-aspartate receptor NMDAR2A subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0002
Polymers31,8521
Non-polymers1471
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: N-methyl-D-aspartate receptor NMDAR2A subunit
hetero molecules

A: N-methyl-D-aspartate receptor NMDAR2A subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9994
Polymers63,7052
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2790 Å2
ΔGint-11 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.106, 52.106, 198.675
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Cell settingtetragonal
Space group name H-MP41212

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Components

#1: 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
#2: Chemical ChemComp-GLU / GLUTAMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.117 Å3/Da / Density % sol: 42 %
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: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 9, 2003
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 30942 / Num. obs: 30725 / % possible obs: 99.3 % / Biso Wilson estimate: 17.5 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: Combination of molecular replacement, SAD
Resolution: 1.7→19.19 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1859072.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.223 3074 10 %RANDOM
Rwork0.196 ---
obs0.1961 30942 98.4 %-
all-30942 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.0422 Å2 / ksol: 0.409777 e/Å3
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2--0.9 Å20 Å2
3----1.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 10 316 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.842
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.272.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 458 9.7 %
Rwork0.215 4249 -
obs--92.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2glut.paramglut.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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